version bump to pre-release

DESCRIPTION

@@ -1,18 +1,18 @@
 Package: MSstatsBioNet
 Type: Package
-Title: Protein-Protein Interaction Analysis for MS-based Proteomics Experiments
-Version: 0.1.0
+Title: Network Analysis for MS-based Proteomics Experiments
+Version: 0.99.0
 Authors@R: c(
     person("Anthony", "Wu", email = "wu.anthon@northeastern.edu", 
         role = c("aut", "cre")),
     person("Olga", "Vitek", email = "o.vitek@northeastern.edu", 
         role = "aut", comment=c(ORCID = "0000-0003-1728-1104"))) 
-Description: A set of tools for protein-protein interaction analysis using mass 
+Description: A set of tools for network analysis using mass 
     spectrometry-based proteomics data and network databases. The package takes 
     as input the output of MSstats differential abundance analysis and provides 
     functions to perform enrichment analysis and visualization in the 
     context of prior knowledge from past literature. Notably, this package 
-    integrates with INDRA, which is a database of protein-protein interactions 
+    integrates with INDRA, which is a database of biological networks
     extracted from the literature using text mining techniques.
 License: Artistic-2.0
 Depends: R (>= 4.4.0)
@@ -30,7 +30,7 @@ Suggests:
     mockery
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, 
-    QualityControl
+    QualityControl, NetworkEnrichment, Network
 Encoding: UTF-8
 URL: http://msstats.org, https://vitek-lab.github.io/MSstatsBioNet/
 BugReports: https://groups.google.com/forum/#!forum/msstats

NEWS.md

@@ -1,3 +1,10 @@
+# MSstatsBioNet 0.99.0
+
+* Added function `getSubnetworkFromIndra` to extract biomolecular subnetworks 
+from the INDRA database.
+* Added function `visualizeNetworks` to visualize networks in Cytoscape desktop.
+* Added vignette
+
 # MSstatsBioNet 0.1.0
 
 * Added a `NEWS.md` file to track changes to the package.

R/visualizeNetworks.R

@@ -23,7 +23,7 @@
 #'
 #'
 visualizeNetworks <- function(nodes, edges,
-                              pvalue_cutoff = 0.05, logfc_cutoff = 0.5) {
+                                pvalue_cutoff = 0.05, logfc_cutoff = 0.5) {
     # Add additional columns for visualization
     nodes$logFC_color <- nodes$logFC
     nodes$logFC_color[nodes$pvalue > pvalue_cutoff |

README.md

@@ -5,6 +5,22 @@
 This package provides a suite of functions to query various network databases, 
 filter queries & results, and visualize networks.
 
+## Installation Instructions
+
+To install this package on bioconductor, run the following command:
+```
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("MSstatsBioNet")
+```
+
+You can install the development version of this package through Github:
+
+```
+devtools::install_github("Vitek-Lab/MSstatsConvert", build_vignettes = TRUE)
+```
+
 ## Databases Supported
 
 - INDRA

vignettes/MSstatsBioNet.Rmd

@@ -19,7 +19,7 @@ library(MSstatsBioNet)
 ```
 
 # Purpose of MSstatsBioNet
-  
+
 The `MSstatsBioNet` package is a member of the `MSstats` family of packages.
 It contains a set of functions for interpretation of mass spectrometry (MS) 
 statistical analysis results in the context of protein-protein interaction 
@@ -40,3 +40,10 @@ input <- data.table::fread(
 subnetwork <- getSubnetworkFromIndra(input)
 visualizeNetworks(subnetwork$nodes, subnetwork$edges)
 ```
+
+
+# Session info
+
+```{r}
+sessionInfo()
+```