From c9816a049236bdd3265677dcf2a8d9f462853592 Mon Sep 17 00:00:00 2001
From: tonywu1999 <anthonywu92@gmail.com>
Date: Wed, 25 Sep 2024 19:31:11 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Vitek-La?=
 =?UTF-8?q?b/MSstatsBioNet@64bec3394399d246ff4d3401dbe9b2d8686914a3=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                              |  4 +-
 LICENSE-text.html                     |  4 +-
 articles/MSstatsBioNet.html           | 72 +++++++++++++--------------
 articles/index.html                   |  4 +-
 authors.html                          |  8 +--
 index.html                            |  4 +-
 news/index.html                       |  4 +-
 pkgdown.js                            |  8 +++
 pkgdown.yml                           |  4 +-
 reference/getSubnetworkFromIndra.html |  4 +-
 reference/index.html                  |  4 +-
 reference/visualizeNetworks.html      |  4 +-
 search.json                           |  2 +-
 13 files changed, 67 insertions(+), 59 deletions(-)

diff --git a/404.html b/404.html
index 3c68411..a2f6de4 100644
--- a/404.html
+++ b/404.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="https://vitek-lab.github.io/MSstatsBioNet/index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -61,7 +61,7 @@ <h1>Page not found (404)</h1>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer>
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 4c1530d..6afd7db 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -146,7 +146,7 @@ <h1>License</h1>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/articles/MSstatsBioNet.html b/articles/MSstatsBioNet.html
index 242ecc9..e38693d 100644
--- a/articles/MSstatsBioNet.html
+++ b/articles/MSstatsBioNet.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -88,24 +88,24 @@ <h2 id="msstats-convert-from-upstream-dataset">MSstats Convert from Upstream Dat
 <span>    annotation <span class="op">=</span> <span class="va">annot</span>,</span>
 <span>    use_log_file <span class="op">=</span> <span class="cn">FALSE</span></span>
 <span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Raw data from Metamorpheus imported successfully.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Raw data from Metamorpheus cleaned successfully.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Using provided annotation.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Run labels were standardized to remove symbols such as '.' or '%'.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** The following options are used:</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Raw data from Metamorpheus imported successfully.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Raw data from Metamorpheus cleaned successfully.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Using provided annotation.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Run labels were standardized to remove symbols such as '.' or '%'.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** The following options are used:</span></span>
 <span><span class="co">#&gt;   - Features will be defined by the columns: PeptideSequence, PrecursorCharge</span></span>
 <span><span class="co">#&gt;   - Shared peptides will be removed.</span></span>
 <span><span class="co">#&gt;   - Proteins with single feature will not be removed.</span></span>
 <span><span class="co">#&gt;   - Features with less than 3 measurements across runs will be removed.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Features with all missing measurements across runs are removed.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Shared peptides are removed.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Features with one or two measurements across runs are removed.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Run annotation merged with quantification data.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Features with one or two measurements across runs are removed.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Fractionation handled.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Updated quantification data to make balanced design. Missing values are marked by NA</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:21] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Features with all missing measurements across runs are removed.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Shared peptides are removed.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Features with one or two measurements across runs are removed.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Run annotation merged with quantification data.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Features with one or two measurements across runs are removed.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Fractionation handled.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Updated quantification data to make balanced design. Missing values are marked by NA</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:04] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">msstats_imported</span><span class="op">)</span></span>
 <span><span class="co">#&gt;   ProteinName                                           PeptideSequence</span></span>
 <span><span class="co">#&gt; 1      O43707 AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR</span></span>
@@ -147,31 +147,31 @@ <h2 id="msstats-process-and-groupcomparison">MSstats Process and GroupComparison
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;     savePlot</span></span>
 <span><span class="va">QuantData</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/MSstats/man/dataProcess.html" class="external-link">dataProcess</a></span><span class="op">(</span><span class="va">msstats_imported</span>, use_log_file <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:22] ** Log2 intensities under cutoff = 16.018  were considered as censored missing values.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:22] ** Log2 intensities = NA were considered as censored missing values.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:22] ** Use all features that the dataset originally has.</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:22] </span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06] ** Log2 intensities under cutoff = 16.018  were considered as censored missing values.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06] ** Log2 intensities = NA were considered as censored missing values.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06] ** Use all features that the dataset originally has.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06] </span></span>
 <span><span class="co">#&gt;  # proteins: 7</span></span>
 <span><span class="co">#&gt;  # peptides per protein: 1-26</span></span>
 <span><span class="co">#&gt;  # features per peptide: 1-1</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:22] Some proteins have only one feature: </span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06] Some proteins have only one feature: </span></span>
 <span><span class="co">#&gt;  O00391 ...</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:22] </span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06] </span></span>
 <span><span class="co">#&gt;                     neg pos</span></span>
 <span><span class="co">#&gt;              # runs   2   2</span></span>
 <span><span class="co">#&gt;     # bioreplicates   2   2</span></span>
 <span><span class="co">#&gt;  # tech. replicates   1   1</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:22]  == Start the summarization per subplot...</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06]  == Start the summarization per subplot...</span></span>
 <span><span class="co">#&gt;   |                                                                              |                                                                      |   0%  |                                                                              |==========                                                            |  14%  |                                                                              |====================                                                  |  29%  |                                                                              |==============================                                        |  43%  |                                                                              |========================================                              |  57%  |                                                                              |==================================================                    |  71%  |                                                                              |============================================================          |  86%  |                                                                              |======================================================================| 100%</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:23]  == Summarization is done.</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06]  == Summarization is done.</span></span>
 <span><span class="va">groupComparisonResult</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/MSstats/man/groupComparison.html" class="external-link">groupComparison</a></span><span class="op">(</span></span>
 <span>    contrast.matrix <span class="op">=</span> <span class="st">"pairwise"</span>,</span>
 <span>    data <span class="op">=</span> <span class="va">QuantData</span>,</span>
 <span>    use_log_file <span class="op">=</span> <span class="cn">FALSE</span></span>
 <span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:23]  == Start to test and get inference in whole plot ...</span></span>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06]  == Start to test and get inference in whole plot ...</span></span>
 <span><span class="co">#&gt;   |                                                                              |                                                                      |   0%  |                                                                              |==========                                                            |  14%  |                                                                              |====================                                                  |  29%  |                                                                              |==============================                                        |  43%  |                                                                              |========================================                              |  57%  |                                                                              |==================================================                    |  71%  |                                                                              |============================================================          |  86%  |                                                                              |======================================================================| 100%</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-04 00:12:23]  == Comparisons for all proteins are done.</span></span></code></pre></div>
+<span><span class="co">#&gt; INFO  [2024-09-25 19:31:06]  == Comparisons for all proteins are done.</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="msstatsbionet-analysis">MSstatsBioNet Analysis<a class="anchor" aria-label="anchor" href="#msstatsbionet-analysis"></a>
@@ -242,7 +242,7 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; R version 4.4.1 (2024-06-14)</span></span>
 <span><span class="co">#&gt; Platform: x86_64-pc-linux-gnu</span></span>
-<span><span class="co">#&gt; Running under: Ubuntu 22.04.4 LTS</span></span>
+<span><span class="co">#&gt; Running under: Ubuntu 22.04.5 LTS</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Matrix products: default</span></span>
 <span><span class="co">#&gt; BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 </span></span>
@@ -261,7 +261,7 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt; [1] MSstats_4.12.1        MSstatsConvert_1.14.0 MSstatsBioNet_0.99.2 </span></span>
+<span><span class="co">#&gt; [1] MSstats_4.12.1        MSstatsConvert_1.14.0 MSstatsBioNet_0.99.3 </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
 <span><span class="co">#&gt;  [1] tidyselect_1.2.1      viridisLite_0.4.2     IRdisplay_1.1        </span></span>
@@ -272,26 +272,26 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; [16] compiler_4.4.1        r2r_0.1.1             rlang_1.1.4          </span></span>
 <span><span class="co">#&gt; [19] sass_0.4.9            tools_4.4.1           utf8_1.2.4           </span></span>
 <span><span class="co">#&gt; [22] yaml_2.3.10           data.table_1.16.0     knitr_1.48           </span></span>
-<span><span class="co">#&gt; [25] htmlwidgets_1.6.4     curl_5.2.2            marray_1.82.0        </span></span>
+<span><span class="co">#&gt; [25] htmlwidgets_1.6.4     curl_5.2.3            marray_1.82.0        </span></span>
 <span><span class="co">#&gt; [28] repr_1.1.7            RColorBrewer_1.1-3    KernSmooth_2.23-24   </span></span>
-<span><span class="co">#&gt; [31] pbdZMQ_0.3-11         purrr_1.0.2           BiocGenerics_0.50.0  </span></span>
+<span><span class="co">#&gt; [31] pbdZMQ_0.3-13         purrr_1.0.2           BiocGenerics_0.50.0  </span></span>
 <span><span class="co">#&gt; [34] desc_1.4.3            grid_4.4.1            stats4_4.4.1         </span></span>
-<span><span class="co">#&gt; [37] preprocessCore_1.66.0 fansi_1.0.6           caTools_1.18.2       </span></span>
+<span><span class="co">#&gt; [37] preprocessCore_1.66.0 fansi_1.0.6           caTools_1.18.3       </span></span>
 <span><span class="co">#&gt; [40] colorspace_2.1-1      log4r_0.4.3           ggplot2_3.5.1        </span></span>
 <span><span class="co">#&gt; [43] scales_1.3.0          gtools_3.9.5          MASS_7.3-60.2        </span></span>
 <span><span class="co">#&gt; [46] cli_3.6.3             rmarkdown_2.28        crayon_1.5.3         </span></span>
-<span><span class="co">#&gt; [49] ragg_1.3.2            generics_0.1.3        httr_1.4.7           </span></span>
+<span><span class="co">#&gt; [49] ragg_1.3.3            generics_0.1.3        httr_1.4.7           </span></span>
 <span><span class="co">#&gt; [52] minqa_1.2.8           cachem_1.1.0          splines_4.4.1        </span></span>
 <span><span class="co">#&gt; [55] parallel_4.4.1        base64enc_0.1-3       vctrs_0.6.5          </span></span>
-<span><span class="co">#&gt; [58] boot_1.3-30           Matrix_1.7-0          jsonlite_1.8.8       </span></span>
-<span><span class="co">#&gt; [61] ggrepel_0.9.5         systemfonts_1.1.0     plotly_4.10.4        </span></span>
+<span><span class="co">#&gt; [58] boot_1.3-30           Matrix_1.7-0          jsonlite_1.8.9       </span></span>
+<span><span class="co">#&gt; [61] ggrepel_0.9.6         systemfonts_1.1.0     plotly_4.10.4        </span></span>
 <span><span class="co">#&gt; [64] limma_3.60.4          tidyr_1.3.1           jquerylib_0.1.4      </span></span>
-<span><span class="co">#&gt; [67] glue_1.7.0            pkgdown_2.1.0         nloptr_2.1.1         </span></span>
+<span><span class="co">#&gt; [67] glue_1.7.0            pkgdown_2.1.1         nloptr_2.1.1         </span></span>
 <span><span class="co">#&gt; [70] RJSONIO_1.3-1.9       stringi_1.8.4         gtable_0.3.5         </span></span>
 <span><span class="co">#&gt; [73] lme4_1.1-35.5         munsell_0.5.1         tibble_3.2.1         </span></span>
 <span><span class="co">#&gt; [76] pillar_1.9.0          htmltools_0.5.8.1     gplots_3.1.3.1       </span></span>
 <span><span class="co">#&gt; [79] RCy3_2.24.0           IRkernel_1.3.2        graph_1.82.0         </span></span>
-<span><span class="co">#&gt; [82] R6_2.5.1              textshaping_0.4.0     evaluate_0.24.0      </span></span>
+<span><span class="co">#&gt; [82] R6_2.5.1              textshaping_0.4.0     evaluate_1.0.0       </span></span>
 <span><span class="co">#&gt; [85] lattice_0.22-6        backports_1.5.0       bslib_0.8.0          </span></span>
 <span><span class="co">#&gt; [88] Rcpp_1.0.13           uuid_1.2-1            nlme_3.1-164         </span></span>
 <span><span class="co">#&gt; [91] checkmate_2.3.2       xfun_0.47             fs_1.6.4             </span></span>
@@ -308,7 +308,7 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer>
diff --git a/articles/index.html b/articles/index.html
index bcd119c..fbf6181 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -46,7 +46,7 @@ <h3>All vignettes</h3>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/authors.html b/authors.html
index 71b25f0..aa13072 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -50,13 +50,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Wu A, Vitek O (2024).
 <em>MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments</em>.
-R package version 0.99.2, https://vitek-lab.github.io/MSstatsBioNet/, <a href="http://msstats.org" class="external-link">http://msstats.org</a>.
+R package version 0.99.3, https://vitek-lab.github.io/MSstatsBioNet/, <a href="http://msstats.org" class="external-link">http://msstats.org</a>.
 </p>
       <pre>@Manual{,
   title = {MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments},
   author = {Anthony Wu and Olga Vitek},
   year = {2024},
-  note = {R package version 0.99.2, https://vitek-lab.github.io/MSstatsBioNet/},
+  note = {R package version 0.99.3, https://vitek-lab.github.io/MSstatsBioNet/},
   url = {http://msstats.org},
 }</pre>
     </div>
@@ -70,7 +70,7 @@ <h2 id="citation">Citation</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/index.html b/index.html
index 47e85b5..bd8ba7d 100644
--- a/index.html
+++ b/index.html
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -132,7 +132,7 @@ <h2 data-toc-skip>Developers</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer>
diff --git a/news/index.html b/news/index.html
index 726fb81..9d36113 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -51,7 +51,7 @@ <h2 class="pkg-version" data-toc-text="0.1.0" id="msstatsbionet-010">MSstatsBioN
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/pkgdown.js b/pkgdown.js
index 9757bf9..1a99c65 100644
--- a/pkgdown.js
+++ b/pkgdown.js
@@ -152,3 +152,11 @@ async function searchFuse(query, callback) {
   });
   });
 })(window.jQuery || window.$)
+
+document.addEventListener('keydown', function(event) {
+  // Check if the pressed key is '/'
+  if (event.key === '/') {
+    event.preventDefault();  // Prevent any default action associated with the '/' key
+    document.getElementById('search-input').focus();  // Set focus to the search input
+  }
+});
diff --git a/pkgdown.yml b/pkgdown.yml
index 0368ff9..85fbafb 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,9 +1,9 @@
 pandoc: 3.1.11
-pkgdown: 2.1.0
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   MSstatsBioNet: MSstatsBioNet.html
-last_built: 2024-09-04T00:12Z
+last_built: 2024-09-25T19:30Z
 urls:
   reference: https://vitek-lab.github.io/MSstatsBioNet/reference
   article: https://vitek-lab.github.io/MSstatsBioNet/articles
diff --git a/reference/getSubnetworkFromIndra.html b/reference/getSubnetworkFromIndra.html
index 28499f3..842c500 100644
--- a/reference/getSubnetworkFromIndra.html
+++ b/reference/getSubnetworkFromIndra.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -91,7 +91,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/reference/index.html b/reference/index.html
index c5e9439..44e8f93 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,7 +63,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/reference/visualizeNetworks.html b/reference/visualizeNetworks.html
index b56d0be..db162dd 100644
--- a/reference/visualizeNetworks.html
+++ b/reference/visualizeNetworks.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.3</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -98,7 +98,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/search.json b/search.json
index 15d0f1d..6e41b48 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"purpose-of-msstatsbionet","dir":"Articles","previous_headings":"","what":"Purpose of MSstatsBioNet","title":"MSstatsBioNet","text":"MSstatsBioNet package member MSstats family packages. contains set functions interpretation mass spectrometry (MS) statistical analysis results context protein-protein interaction networks. package designed used conjunction MSstats package.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"msstats-convert-from-upstream-dataset","dir":"Articles","previous_headings":"","what":"MSstats Convert from Upstream Dataset","title":"MSstatsBioNet","text":"","code":"library(MSstatsConvert) input <- system.file(\"tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv\",     package = \"MSstatsConvert\" ) input <- data.table::fread(input) annot <- system.file(\"tinytest/raw_data/Metamorpheus/Annotation.tsv\",     package = \"MSstatsConvert\" ) annot <- data.table::fread(annot) msstats_imported <- MetamorpheusToMSstatsFormat(input,     annotation = annot,     use_log_file = FALSE ) #> INFO  [2024-09-04 00:12:21] ** Raw data from Metamorpheus imported successfully. #> INFO  [2024-09-04 00:12:21] ** Raw data from Metamorpheus cleaned successfully. #> INFO  [2024-09-04 00:12:21] ** Using provided annotation. #> INFO  [2024-09-04 00:12:21] ** Run labels were standardized to remove symbols such as '.' or '%'. #> INFO  [2024-09-04 00:12:21] ** The following options are used: #>   - Features will be defined by the columns: PeptideSequence, PrecursorCharge #>   - Shared peptides will be removed. #>   - Proteins with single feature will not be removed. #>   - Features with less than 3 measurements across runs will be removed. #> INFO  [2024-09-04 00:12:21] ** Features with all missing measurements across runs are removed. #> INFO  [2024-09-04 00:12:21] ** Shared peptides are removed. #> INFO  [2024-09-04 00:12:21] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max #> INFO  [2024-09-04 00:12:21] ** Features with one or two measurements across runs are removed. #> INFO  [2024-09-04 00:12:21] ** Run annotation merged with quantification data. #> INFO  [2024-09-04 00:12:21] ** Features with one or two measurements across runs are removed. #> INFO  [2024-09-04 00:12:21] ** Fractionation handled. #> INFO  [2024-09-04 00:12:21] ** Updated quantification data to make balanced design. Missing values are marked by NA #> INFO  [2024-09-04 00:12:21] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. head(msstats_imported) #>   ProteinName                                           PeptideSequence #> 1      O43707 AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR #> 2      O43707 AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR #> 3      O43707 AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR #> 4      O43707 AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR #> 5      B9A064                                                AGVETTKPSK #> 6      B9A064                                                AGVETTKPSK #>   PrecursorCharge FragmentIon ProductCharge IsotopeLabelType Condition #> 1               3          NA            NA                L       neg #> 2               3          NA            NA                L       neg #> 3               3          NA            NA                L       pos #> 4               3          NA            NA                L       pos #> 5               2          NA            NA                L       neg #> 6               2          NA            NA                L       neg #>   BioReplicate        Run Fraction Intensity #> 1            1 NEG1-calib        1        NA #> 2            2 NEG2-calib        1  655481.2 #> 3            3 POS1-calib        1  496891.9 #> 4            4 POS2-calib        1  213691.0 #> 5            1 NEG1-calib        1 4201663.3 #> 6            2 NEG2-calib        1 4427577.4"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"msstats-process-and-groupcomparison","dir":"Articles","previous_headings":"","what":"MSstats Process and GroupComparison","title":"MSstatsBioNet","text":"","code":"library(MSstats) #>  #> Attaching package: 'MSstats' #> The following objects are masked from 'package:MSstatsConvert': #>  #>     DIANNtoMSstatsFormat, DIAUmpiretoMSstatsFormat, #>     FragPipetoMSstatsFormat, MaxQtoMSstatsFormat, #>     OpenMStoMSstatsFormat, OpenSWATHtoMSstatsFormat, PDtoMSstatsFormat, #>     ProgenesistoMSstatsFormat, SkylinetoMSstatsFormat, #>     SpectronauttoMSstatsFormat #> The following object is masked from 'package:grDevices': #>  #>     savePlot QuantData <- dataProcess(msstats_imported, use_log_file = FALSE) #> INFO  [2024-09-04 00:12:22] ** Log2 intensities under cutoff = 16.018  were considered as censored missing values. #> INFO  [2024-09-04 00:12:22] ** Log2 intensities = NA were considered as censored missing values. #> INFO  [2024-09-04 00:12:22] ** Use all features that the dataset originally has. #> INFO  [2024-09-04 00:12:22]  #>  # proteins: 7 #>  # peptides per protein: 1-26 #>  # features per peptide: 1-1 #> INFO  [2024-09-04 00:12:22] Some proteins have only one feature:  #>  O00391 ... #> INFO  [2024-09-04 00:12:22]  #>                     neg pos #>              # runs   2   2 #>     # bioreplicates   2   2 #>  # tech. replicates   1   1 #> INFO  [2024-09-04 00:12:22]  == Start the summarization per subplot... #>   |                                                                              |                                                                      |   0%  |                                                                              |==========                                                            |  14%  |                                                                              |====================                                                  |  29%  |                                                                              |==============================                                        |  43%  |                                                                              |========================================                              |  57%  |                                                                              |==================================================                    |  71%  |                                                                              |============================================================          |  86%  |                                                                              |======================================================================| 100% #> INFO  [2024-09-04 00:12:23]  == Summarization is done. groupComparisonResult <- groupComparison(     contrast.matrix = \"pairwise\",     data = QuantData,     use_log_file = FALSE ) #> INFO  [2024-09-04 00:12:23]  == Start to test and get inference in whole plot ... #>   |                                                                              |                                                                      |   0%  |                                                                              |==========                                                            |  14%  |                                                                              |====================                                                  |  29%  |                                                                              |==============================                                        |  43%  |                                                                              |========================================                              |  57%  |                                                                              |==================================================                    |  71%  |                                                                              |============================================================          |  86%  |                                                                              |======================================================================| 100% #> INFO  [2024-09-04 00:12:23]  == Comparisons for all proteins are done."},{"path":[]},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"id-conversion","dir":"Articles","previous_headings":"MSstatsBioNet Analysis","what":"ID Conversion","title":"MSstatsBioNet","text":"First, need convert group comparison results format can processed INDRA. getSubnetworkFromIndra function requires table containing HGNC IDs. can use following mapping convert Uniprot HGNC ID. mapping obtained Python uniprot client future, uniprot client added separate function allow users perform conversion R streamlined way.","code":"uniprot_to_hgnc_mapping <- c(     \"B9A064\" = \"38476\",     \"O00391\" = \"9756\",     \"O14818\" = \"9536\",     \"O43598\" = \"21218\",     \"O43707\" = \"166\",     \"P16050\" = \"11390\",     \"P84243\" = \"4765\" ) groupComparisonResult$ComparisonResult$HgncId <- uniprot_to_hgnc_mapping[     groupComparisonResult$ComparisonResult$Protein ]"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"subnetwork-query","dir":"Articles","previous_headings":"MSstatsBioNet Analysis","what":"Subnetwork Query","title":"MSstatsBioNet","text":"package provides function getSubnetworkFromIndra retrieves subnetwork proteins INDRA database based differential abundance analysis results. package distributed Artistic-2.0 license. However, dependencies may different licenses. example, getSubnetworkFromIndra depends INDRA, distributed BSD 2-Clause license. Furthermore, INDRA’s knowledge sources may different licenses commercial applications. Please refer INDRA README information knowledge sources associated licenses.","code":"subnetwork <- getSubnetworkFromIndra(groupComparisonResult$ComparisonResult) #> Warning in getSubnetworkFromIndra(groupComparisonResult$ComparisonResult): NOTICE: This function includes third-party software components #>         that are licensed under the BSD 2-Clause License. Please ensure to #>         include the third-party licensing agreements if redistributing this #>         package or utilizing the results based on this package. #>         See the LICENSE file for more details."},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"visualize-networks","dir":"Articles","previous_headings":"MSstatsBioNet Analysis","what":"Visualize Networks","title":"MSstatsBioNet","text":"function visualizeNetworks takes output getSubnetworkFromIndra visualizes subnetwork.","code":"visualizeNetworks(subnetwork$nodes, subnetwork$edges) #> Warning in visualizeNetworks(subnetwork$nodes, subnetwork$edges): Visualization #> is not available in non-interactive mode."},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"MSstatsBioNet","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] MSstats_4.12.1        MSstatsConvert_1.14.0 MSstatsBioNet_0.99.2  #>  #> loaded via a namespace (and not attached): #>  [1] tidyselect_1.2.1      viridisLite_0.4.2     IRdisplay_1.1         #>  [4] dplyr_1.1.4           bitops_1.0-8          lazyeval_0.2.2        #>  [7] fastmap_1.2.0         RCurl_1.98-1.16       XML_3.99-0.17         #> [10] digest_0.6.37         base64url_1.4         lifecycle_1.0.4       #> [13] survival_3.6-4        statmod_1.5.0         magrittr_2.0.3        #> [16] compiler_4.4.1        r2r_0.1.1             rlang_1.1.4           #> [19] sass_0.4.9            tools_4.4.1           utf8_1.2.4            #> [22] yaml_2.3.10           data.table_1.16.0     knitr_1.48            #> [25] htmlwidgets_1.6.4     curl_5.2.2            marray_1.82.0         #> [28] repr_1.1.7            RColorBrewer_1.1-3    KernSmooth_2.23-24    #> [31] pbdZMQ_0.3-11         purrr_1.0.2           BiocGenerics_0.50.0   #> [34] desc_1.4.3            grid_4.4.1            stats4_4.4.1          #> [37] preprocessCore_1.66.0 fansi_1.0.6           caTools_1.18.2        #> [40] colorspace_2.1-1      log4r_0.4.3           ggplot2_3.5.1         #> [43] scales_1.3.0          gtools_3.9.5          MASS_7.3-60.2         #> [46] cli_3.6.3             rmarkdown_2.28        crayon_1.5.3          #> [49] ragg_1.3.2            generics_0.1.3        httr_1.4.7            #> [52] minqa_1.2.8           cachem_1.1.0          splines_4.4.1         #> [55] parallel_4.4.1        base64enc_0.1-3       vctrs_0.6.5           #> [58] boot_1.3-30           Matrix_1.7-0          jsonlite_1.8.8        #> [61] ggrepel_0.9.5         systemfonts_1.1.0     plotly_4.10.4         #> [64] limma_3.60.4          tidyr_1.3.1           jquerylib_0.1.4       #> [67] glue_1.7.0            pkgdown_2.1.0         nloptr_2.1.1          #> [70] RJSONIO_1.3-1.9       stringi_1.8.4         gtable_0.3.5          #> [73] lme4_1.1-35.5         munsell_0.5.1         tibble_3.2.1          #> [76] pillar_1.9.0          htmltools_0.5.8.1     gplots_3.1.3.1        #> [79] RCy3_2.24.0           IRkernel_1.3.2        graph_1.82.0          #> [82] R6_2.5.1              textshaping_0.4.0     evaluate_0.24.0       #> [85] lattice_0.22-6        backports_1.5.0       bslib_0.8.0           #> [88] Rcpp_1.0.13           uuid_1.2-1            nlme_3.1-164          #> [91] checkmate_2.3.2       xfun_0.47             fs_1.6.4              #> [94] pkgconfig_2.0.3"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anthony Wu. Author, maintainer. Olga Vitek. Author.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wu , Vitek O (2024). MSstatsBioNet: Network Analysis MS-based Proteomics Experiments. R package version 0.99.2, https://vitek-lab.github.io/MSstatsBioNet/, http://msstats.org.","code":"@Manual{,   title = {MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments},   author = {Anthony Wu and Olga Vitek},   year = {2024},   note = {R package version 0.99.2, https://vitek-lab.github.io/MSstatsBioNet/},   url = {http://msstats.org}, }"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"msstatsbionet","dir":"","previous_headings":"","what":"Network Analysis for MS-based Proteomics Experiments","title":"Network Analysis for MS-based Proteomics Experiments","text":"package provides suite functions query various network databases, filter queries & results, visualize networks.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"installation-instructions","dir":"","previous_headings":"","what":"Installation Instructions","title":"Network Analysis for MS-based Proteomics Experiments","text":"install package bioconductor, run following command: can install development version package Github:","code":"if (!require(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\")  BiocManager::install(\"MSstatsBioNet\") devtools::install_github(\"Vitek-Lab/MSstatsConvert\", build_vignettes = TRUE)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Network Analysis for MS-based Proteomics Experiments","text":"package distributed Artistic-2.0 license. However, dependencies may different licenses. Notably, INDRA distributed BSD 2-Clause license. Furthermore, INDRA’s knowledge sources may different licenses commercial applications. Please refer INDRA README information knowledge sources associated licenses.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"databases-supported","dir":"","previous_headings":"","what":"Databases Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"INDRA","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"filtering-options-supported","dir":"","previous_headings":"","what":"Filtering Options Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"P-Value Filter","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"visualization-options-supported","dir":"","previous_headings":"","what":"Visualization Options Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"Cytoscape Desktop","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":null,"dir":"Reference","previous_headings":"","what":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"Get subnetwork INDRA database differential analysis results","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"","code":"getSubnetworkFromIndra(input, pvalue_cutoff = NULL)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"input groupComparison comparisionResult table additional HGNC ID HGNC name columns pvalue_cutoff p-value cutoff filtering. Default NULL, .e. filtering","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"list 2 data.frames, nodes edges","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"","code":"input <- data.table::fread(system.file(     \"extdata/groupComparisonModel.csv\",     package = \"MSstatsBioNet\" )) subnetwork <- getSubnetworkFromIndra(input, pvalue_cutoff = 0.05) #> Warning: NOTICE: This function includes third-party software components #>         that are licensed under the BSD 2-Clause License. Please ensure to #>         include the third-party licensing agreements if redistributing this #>         package or utilizing the results based on this package. #>         See the LICENSE file for more details. head(subnetwork$nodes) #> [1] id     logFC  pvalue #> <0 rows> (or 0-length row.names) head(subnetwork$edges) #> [1] source        target        interaction   evidenceCount evidenceLink  #> <0 rows> (or 0-length row.names)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"Create visualization network Cytoscape Desktop.  Note Cytoscape Desktop app must open function work.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"","code":"visualizeNetworks(nodes, edges, pvalue_cutoff = 0.05, logfc_cutoff = 0.5)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"nodes dataframe nodes edges dataframe edges pvalue_cutoff p-value cutoff coloring significant proteins. Default 0.05 logfc_cutoff log fold change cutoff coloring significant proteins. Default 0.5","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"cytoscape visualization subnetwork","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"","code":"input <- data.table::fread(system.file(     \"extdata/groupComparisonModel.csv\",     package = \"MSstatsBioNet\" )) subnetwork <- getSubnetworkFromIndra(input) #> Warning: NOTICE: This function includes third-party software components #>         that are licensed under the BSD 2-Clause License. Please ensure to #>         include the third-party licensing agreements if redistributing this #>         package or utilizing the results based on this package. #>         See the LICENSE file for more details. visualizeNetworks(subnetwork$nodes, subnetwork$edges) #> Warning: Visualization is not available in non-interactive mode."},{"path":"https://vitek-lab.github.io/MSstatsBioNet/news/index.html","id":"msstatsbionet-0990","dir":"Changelog","previous_headings":"","what":"MSstatsBioNet 0.99.0","title":"MSstatsBioNet 0.99.0","text":"Added function getSubnetworkFromIndra extract biomolecular subnetworks INDRA database. Added function visualizeNetworks visualize networks Cytoscape desktop. Added vignette","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/news/index.html","id":"msstatsbionet-010","dir":"Changelog","previous_headings":"","what":"MSstatsBioNet 0.1.0","title":"MSstatsBioNet 0.1.0","text":"Added NEWS.md file track changes package.","code":""}]
+[{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"purpose-of-msstatsbionet","dir":"Articles","previous_headings":"","what":"Purpose of MSstatsBioNet","title":"MSstatsBioNet","text":"MSstatsBioNet package member MSstats family packages. contains set functions interpretation mass spectrometry (MS) statistical analysis results context protein-protein interaction networks. package designed used conjunction MSstats package.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"msstats-convert-from-upstream-dataset","dir":"Articles","previous_headings":"","what":"MSstats Convert from Upstream Dataset","title":"MSstatsBioNet","text":"","code":"library(MSstatsConvert) input <- system.file(\"tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv\",     package = \"MSstatsConvert\" ) input <- data.table::fread(input) annot <- system.file(\"tinytest/raw_data/Metamorpheus/Annotation.tsv\",     package = \"MSstatsConvert\" ) annot <- data.table::fread(annot) msstats_imported <- MetamorpheusToMSstatsFormat(input,     annotation = annot,     use_log_file = FALSE ) #> INFO  [2024-09-25 19:31:04] ** Raw data from Metamorpheus imported successfully. #> INFO  [2024-09-25 19:31:04] ** Raw data from Metamorpheus cleaned successfully. #> INFO  [2024-09-25 19:31:04] ** Using provided annotation. #> INFO  [2024-09-25 19:31:04] ** Run labels were standardized to remove symbols such as '.' or '%'. #> INFO  [2024-09-25 19:31:04] ** The following options are used: #>   - Features will be defined by the columns: PeptideSequence, PrecursorCharge #>   - Shared peptides will be removed. #>   - Proteins with single feature will not be removed. #>   - Features with less than 3 measurements across runs will be removed. #> INFO  [2024-09-25 19:31:04] ** Features with all missing measurements across runs are removed. #> INFO  [2024-09-25 19:31:04] ** Shared peptides are removed. #> INFO  [2024-09-25 19:31:04] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max #> INFO  [2024-09-25 19:31:04] ** Features with one or two measurements across runs are removed. #> INFO  [2024-09-25 19:31:04] ** Run annotation merged with quantification data. #> INFO  [2024-09-25 19:31:04] ** Features with one or two measurements across runs are removed. #> INFO  [2024-09-25 19:31:04] ** Fractionation handled. #> INFO  [2024-09-25 19:31:04] ** Updated quantification data to make balanced design. Missing values are marked by NA #> INFO  [2024-09-25 19:31:04] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. head(msstats_imported) #>   ProteinName                                           PeptideSequence #> 1      O43707 AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR #> 2      O43707 AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR #> 3      O43707 AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR #> 4      O43707 AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR #> 5      B9A064                                                AGVETTKPSK #> 6      B9A064                                                AGVETTKPSK #>   PrecursorCharge FragmentIon ProductCharge IsotopeLabelType Condition #> 1               3          NA            NA                L       neg #> 2               3          NA            NA                L       neg #> 3               3          NA            NA                L       pos #> 4               3          NA            NA                L       pos #> 5               2          NA            NA                L       neg #> 6               2          NA            NA                L       neg #>   BioReplicate        Run Fraction Intensity #> 1            1 NEG1-calib        1        NA #> 2            2 NEG2-calib        1  655481.2 #> 3            3 POS1-calib        1  496891.9 #> 4            4 POS2-calib        1  213691.0 #> 5            1 NEG1-calib        1 4201663.3 #> 6            2 NEG2-calib        1 4427577.4"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"msstats-process-and-groupcomparison","dir":"Articles","previous_headings":"","what":"MSstats Process and GroupComparison","title":"MSstatsBioNet","text":"","code":"library(MSstats) #>  #> Attaching package: 'MSstats' #> The following objects are masked from 'package:MSstatsConvert': #>  #>     DIANNtoMSstatsFormat, DIAUmpiretoMSstatsFormat, #>     FragPipetoMSstatsFormat, MaxQtoMSstatsFormat, #>     OpenMStoMSstatsFormat, OpenSWATHtoMSstatsFormat, PDtoMSstatsFormat, #>     ProgenesistoMSstatsFormat, SkylinetoMSstatsFormat, #>     SpectronauttoMSstatsFormat #> The following object is masked from 'package:grDevices': #>  #>     savePlot QuantData <- dataProcess(msstats_imported, use_log_file = FALSE) #> INFO  [2024-09-25 19:31:06] ** Log2 intensities under cutoff = 16.018  were considered as censored missing values. #> INFO  [2024-09-25 19:31:06] ** Log2 intensities = NA were considered as censored missing values. #> INFO  [2024-09-25 19:31:06] ** Use all features that the dataset originally has. #> INFO  [2024-09-25 19:31:06]  #>  # proteins: 7 #>  # peptides per protein: 1-26 #>  # features per peptide: 1-1 #> INFO  [2024-09-25 19:31:06] Some proteins have only one feature:  #>  O00391 ... #> INFO  [2024-09-25 19:31:06]  #>                     neg pos #>              # runs   2   2 #>     # bioreplicates   2   2 #>  # tech. replicates   1   1 #> INFO  [2024-09-25 19:31:06]  == Start the summarization per subplot... #>   |                                                                              |                                                                      |   0%  |                                                                              |==========                                                            |  14%  |                                                                              |====================                                                  |  29%  |                                                                              |==============================                                        |  43%  |                                                                              |========================================                              |  57%  |                                                                              |==================================================                    |  71%  |                                                                              |============================================================          |  86%  |                                                                              |======================================================================| 100% #> INFO  [2024-09-25 19:31:06]  == Summarization is done. groupComparisonResult <- groupComparison(     contrast.matrix = \"pairwise\",     data = QuantData,     use_log_file = FALSE ) #> INFO  [2024-09-25 19:31:06]  == Start to test and get inference in whole plot ... #>   |                                                                              |                                                                      |   0%  |                                                                              |==========                                                            |  14%  |                                                                              |====================                                                  |  29%  |                                                                              |==============================                                        |  43%  |                                                                              |========================================                              |  57%  |                                                                              |==================================================                    |  71%  |                                                                              |============================================================          |  86%  |                                                                              |======================================================================| 100% #> INFO  [2024-09-25 19:31:06]  == Comparisons for all proteins are done."},{"path":[]},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"id-conversion","dir":"Articles","previous_headings":"MSstatsBioNet Analysis","what":"ID Conversion","title":"MSstatsBioNet","text":"First, need convert group comparison results format can processed INDRA. getSubnetworkFromIndra function requires table containing HGNC IDs. can use following mapping convert Uniprot HGNC ID. mapping obtained Python uniprot client future, uniprot client added separate function allow users perform conversion R streamlined way.","code":"uniprot_to_hgnc_mapping <- c(     \"B9A064\" = \"38476\",     \"O00391\" = \"9756\",     \"O14818\" = \"9536\",     \"O43598\" = \"21218\",     \"O43707\" = \"166\",     \"P16050\" = \"11390\",     \"P84243\" = \"4765\" ) groupComparisonResult$ComparisonResult$HgncId <- uniprot_to_hgnc_mapping[     groupComparisonResult$ComparisonResult$Protein ]"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"subnetwork-query","dir":"Articles","previous_headings":"MSstatsBioNet Analysis","what":"Subnetwork Query","title":"MSstatsBioNet","text":"package provides function getSubnetworkFromIndra retrieves subnetwork proteins INDRA database based differential abundance analysis results. package distributed Artistic-2.0 license. However, dependencies may different licenses. example, getSubnetworkFromIndra depends INDRA, distributed BSD 2-Clause license. Furthermore, INDRA’s knowledge sources may different licenses commercial applications. Please refer INDRA README information knowledge sources associated licenses.","code":"subnetwork <- getSubnetworkFromIndra(groupComparisonResult$ComparisonResult) #> Warning in getSubnetworkFromIndra(groupComparisonResult$ComparisonResult): NOTICE: This function includes third-party software components #>         that are licensed under the BSD 2-Clause License. Please ensure to #>         include the third-party licensing agreements if redistributing this #>         package or utilizing the results based on this package. #>         See the LICENSE file for more details."},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"visualize-networks","dir":"Articles","previous_headings":"MSstatsBioNet Analysis","what":"Visualize Networks","title":"MSstatsBioNet","text":"function visualizeNetworks takes output getSubnetworkFromIndra visualizes subnetwork.","code":"visualizeNetworks(subnetwork$nodes, subnetwork$edges) #> Warning in visualizeNetworks(subnetwork$nodes, subnetwork$edges): Visualization #> is not available in non-interactive mode."},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"MSstatsBioNet","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.5 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] MSstats_4.12.1        MSstatsConvert_1.14.0 MSstatsBioNet_0.99.3  #>  #> loaded via a namespace (and not attached): #>  [1] tidyselect_1.2.1      viridisLite_0.4.2     IRdisplay_1.1         #>  [4] dplyr_1.1.4           bitops_1.0-8          lazyeval_0.2.2        #>  [7] fastmap_1.2.0         RCurl_1.98-1.16       XML_3.99-0.17         #> [10] digest_0.6.37         base64url_1.4         lifecycle_1.0.4       #> [13] survival_3.6-4        statmod_1.5.0         magrittr_2.0.3        #> [16] compiler_4.4.1        r2r_0.1.1             rlang_1.1.4           #> [19] sass_0.4.9            tools_4.4.1           utf8_1.2.4            #> [22] yaml_2.3.10           data.table_1.16.0     knitr_1.48            #> [25] htmlwidgets_1.6.4     curl_5.2.3            marray_1.82.0         #> [28] repr_1.1.7            RColorBrewer_1.1-3    KernSmooth_2.23-24    #> [31] pbdZMQ_0.3-13         purrr_1.0.2           BiocGenerics_0.50.0   #> [34] desc_1.4.3            grid_4.4.1            stats4_4.4.1          #> [37] preprocessCore_1.66.0 fansi_1.0.6           caTools_1.18.3        #> [40] colorspace_2.1-1      log4r_0.4.3           ggplot2_3.5.1         #> [43] scales_1.3.0          gtools_3.9.5          MASS_7.3-60.2         #> [46] cli_3.6.3             rmarkdown_2.28        crayon_1.5.3          #> [49] ragg_1.3.3            generics_0.1.3        httr_1.4.7            #> [52] minqa_1.2.8           cachem_1.1.0          splines_4.4.1         #> [55] parallel_4.4.1        base64enc_0.1-3       vctrs_0.6.5           #> [58] boot_1.3-30           Matrix_1.7-0          jsonlite_1.8.9        #> [61] ggrepel_0.9.6         systemfonts_1.1.0     plotly_4.10.4         #> [64] limma_3.60.4          tidyr_1.3.1           jquerylib_0.1.4       #> [67] glue_1.7.0            pkgdown_2.1.1         nloptr_2.1.1          #> [70] RJSONIO_1.3-1.9       stringi_1.8.4         gtable_0.3.5          #> [73] lme4_1.1-35.5         munsell_0.5.1         tibble_3.2.1          #> [76] pillar_1.9.0          htmltools_0.5.8.1     gplots_3.1.3.1        #> [79] RCy3_2.24.0           IRkernel_1.3.2        graph_1.82.0          #> [82] R6_2.5.1              textshaping_0.4.0     evaluate_1.0.0        #> [85] lattice_0.22-6        backports_1.5.0       bslib_0.8.0           #> [88] Rcpp_1.0.13           uuid_1.2-1            nlme_3.1-164          #> [91] checkmate_2.3.2       xfun_0.47             fs_1.6.4              #> [94] pkgconfig_2.0.3"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anthony Wu. Author, maintainer. Olga Vitek. Author.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wu , Vitek O (2024). MSstatsBioNet: Network Analysis MS-based Proteomics Experiments. R package version 0.99.3, https://vitek-lab.github.io/MSstatsBioNet/, http://msstats.org.","code":"@Manual{,   title = {MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments},   author = {Anthony Wu and Olga Vitek},   year = {2024},   note = {R package version 0.99.3, https://vitek-lab.github.io/MSstatsBioNet/},   url = {http://msstats.org}, }"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"msstatsbionet","dir":"","previous_headings":"","what":"Network Analysis for MS-based Proteomics Experiments","title":"Network Analysis for MS-based Proteomics Experiments","text":"package provides suite functions query various network databases, filter queries & results, visualize networks.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"installation-instructions","dir":"","previous_headings":"","what":"Installation Instructions","title":"Network Analysis for MS-based Proteomics Experiments","text":"install package bioconductor, run following command: can install development version package Github:","code":"if (!require(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\")  BiocManager::install(\"MSstatsBioNet\") devtools::install_github(\"Vitek-Lab/MSstatsConvert\", build_vignettes = TRUE)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Network Analysis for MS-based Proteomics Experiments","text":"package distributed Artistic-2.0 license. However, dependencies may different licenses. Notably, INDRA distributed BSD 2-Clause license. Furthermore, INDRA’s knowledge sources may different licenses commercial applications. Please refer INDRA README information knowledge sources associated licenses.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"databases-supported","dir":"","previous_headings":"","what":"Databases Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"INDRA","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"filtering-options-supported","dir":"","previous_headings":"","what":"Filtering Options Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"P-Value Filter","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"visualization-options-supported","dir":"","previous_headings":"","what":"Visualization Options Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"Cytoscape Desktop","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":null,"dir":"Reference","previous_headings":"","what":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"Get subnetwork INDRA database differential analysis results","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"","code":"getSubnetworkFromIndra(input, pvalue_cutoff = NULL)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"input groupComparison comparisionResult table additional HGNC ID HGNC name columns pvalue_cutoff p-value cutoff filtering. Default NULL, .e. filtering","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"list 2 data.frames, nodes edges","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"","code":"input <- data.table::fread(system.file(     \"extdata/groupComparisonModel.csv\",     package = \"MSstatsBioNet\" )) subnetwork <- getSubnetworkFromIndra(input, pvalue_cutoff = 0.05) #> Warning: NOTICE: This function includes third-party software components #>         that are licensed under the BSD 2-Clause License. Please ensure to #>         include the third-party licensing agreements if redistributing this #>         package or utilizing the results based on this package. #>         See the LICENSE file for more details. head(subnetwork$nodes) #> [1] id     logFC  pvalue #> <0 rows> (or 0-length row.names) head(subnetwork$edges) #> [1] source        target        interaction   evidenceCount evidenceLink  #> <0 rows> (or 0-length row.names)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"Create visualization network Cytoscape Desktop.  Note Cytoscape Desktop app must open function work.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"","code":"visualizeNetworks(nodes, edges, pvalue_cutoff = 0.05, logfc_cutoff = 0.5)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"nodes dataframe nodes edges dataframe edges pvalue_cutoff p-value cutoff coloring significant proteins. Default 0.05 logfc_cutoff log fold change cutoff coloring significant proteins. Default 0.5","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"cytoscape visualization subnetwork","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create visualization of network in Cytoscape Desktop. Note that the Cytoscape Desktop app must be open for this function to work. — visualizeNetworks","text":"","code":"input <- data.table::fread(system.file(     \"extdata/groupComparisonModel.csv\",     package = \"MSstatsBioNet\" )) subnetwork <- getSubnetworkFromIndra(input) #> Warning: NOTICE: This function includes third-party software components #>         that are licensed under the BSD 2-Clause License. Please ensure to #>         include the third-party licensing agreements if redistributing this #>         package or utilizing the results based on this package. #>         See the LICENSE file for more details. visualizeNetworks(subnetwork$nodes, subnetwork$edges) #> Warning: Visualization is not available in non-interactive mode."},{"path":"https://vitek-lab.github.io/MSstatsBioNet/news/index.html","id":"msstatsbionet-0990","dir":"Changelog","previous_headings":"","what":"MSstatsBioNet 0.99.0","title":"MSstatsBioNet 0.99.0","text":"Added function getSubnetworkFromIndra extract biomolecular subnetworks INDRA database. Added function visualizeNetworks visualize networks Cytoscape desktop. Added vignette","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/news/index.html","id":"msstatsbionet-010","dir":"Changelog","previous_headings":"","what":"MSstatsBioNet 0.1.0","title":"MSstatsBioNet 0.1.0","text":"Added NEWS.md file track changes package.","code":""}]