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Fix dependencies
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howardbaik committed Jul 8, 2024
1 parent de64a70 commit 85c0e44
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6 changes: 3 additions & 3 deletions DESCRIPTION
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Expand Up @@ -22,17 +22,17 @@ URL: https://github.com/FredHutch/gimap
BugReports: https://github.com/FredHutch/gimap/issues
Imports:
readr,
dplyr,
tidyr,
knitr,
rmarkdown,
rcmdcheck,
ggplot2,
magrittr,
kableExtra,
magrittr,
kableExtra,
pheatmap,
purrr,
janitor,
dplyr
Suggests:
testthat (>= 3.0.0),
roxygen2,
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3 changes: 3 additions & 0 deletions NAMESPACE
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Expand Up @@ -11,8 +11,11 @@ export(setup_data)
import(ggplot2)
import(kableExtra)
importFrom(dplyr,across)
importFrom(dplyr,group_by)
importFrom(dplyr,if_any)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(janitor,clean_names)
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2 changes: 0 additions & 2 deletions R/01-qc.R
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Expand Up @@ -10,8 +10,6 @@
#' @param ... additional parameters are sent to `rmarkdown::render()`
#' @returns a QC report saved locally
#' @export
#' @importFrom tidyr pivot_longer
#' @importFrom magrittr %>%
#' @examples \dontrun{
#'
#' gimap_dataset <- get_example_data("gimap")
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9 changes: 0 additions & 9 deletions R/02-filter.R
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Expand Up @@ -9,7 +9,6 @@
#' @param cutoff default is NULL, relates to the low_plasmid_cpm filter; the cutoff for low log2 CPM values for the plasmid time period; if not specified, The lower outlier (defined by taking the difference of the lower quartile and 1.5 * interquartile range) is used
#' @param min_n_filters default is 1; this parameter defines at least how many/the minimum number of independent filters have to flag a pgRNA construct before the construct is filtered when using a combination of filters
#' You should decide on the appropriate filter based on the results of your QC report.
#' @importFrom purrr reduce
#' @returns a filtered version of the gimap_dataset returned in the $filtered_data section
#' filter_step_run is a boolean reporting if the filter step was run or not (since it's optional)
#' metadata_pg_ids is a subset the pgRNA IDs such that these are the ones that remain in the dataset following completion of filtering
Expand Down Expand Up @@ -135,9 +134,6 @@ gimap_filter <- function(.data = NULL,
#' @description This function flags and reports which and how many pgRNAs have a raw count of 0 for any sample/time point
#' @param gimap_dataset The special gimap_dataset from the `setup_data` function which contains the raw count data
#' @param filter_zerocount_target_col default is NULL; Which sample column(s) should be used to check for counts of 0? If NULL and not specified, downstream analysis will select all sample columns
#' @importFrom magrittr %>%
#' @importFrom dplyr mutate
#' @importFrom purrr reduce map
#' @return a named list with the filter `filter` specifying which pgRNA have a count zero for at least one sample/time point and a report df `reportdf` for the number and percent of pgRNA which have a count zero for at least one sample/time point
#' @examples \dontrun{
#' gimap_dataset <- get_example_data("gimap")
Expand Down Expand Up @@ -172,10 +168,6 @@ qc_filter_zerocounts <- function(gimap_dataset, filter_zerocount_target_col = NU
#' @param gimap_dataset The special gimap_dataset from the `setup_data` function which contains the log2 CPM transformed data
#' @param cutoff default is NULL, the cutoff for low log2 CPM values for the plasmid time period; if not specified, The lower outlier (defined by taking the difference of the lower quartile and 1.5 * interquartile range) is used
#' @param filter_plasmid_target_col default is NULL, and if NULL, will select the first column only; this parameter specifically should be used to specify the plasmid column(s) that will be selected
#' @importFrom magrittr %>%
#' @importFrom dplyr mutate across if_any
#' @importFrom tidyr pivot_wider pivot_longer
#' @importFrom janitor clean_names
#' @return a named list with the filter `filter` specifying which pgRNAs have low plasmid log2 CPM (column of interest is `plasmid_cpm_filter`) and a report df `reportdf` for the number and percent of pgRNA which have a low plasmid log2 CPM
#' @examples \dontrun{
#' gimap_dataset <- get_example_data("gimap")
Expand All @@ -193,7 +185,6 @@ qc_filter_zerocounts <- function(gimap_dataset, filter_zerocount_target_col = NU
#'
#' }
#'

qc_filter_plasmid <- function(gimap_dataset, cutoff = NULL, filter_plasmid_target_col = NULL){

if (is.null(filter_plasmid_target_col)) {filter_plasmid_target_col <- c(1)}
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12 changes: 12 additions & 0 deletions R/gimap-package.R
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@@ -0,0 +1,12 @@
#' @keywords internal
"_PACKAGE"

## usethis namespace: start
#' @importFrom dplyr across if_any mutate select summarize
#' @importFrom dplyr group_by
#' @importFrom janitor clean_names
#' @importFrom magrittr %>%
#' @importFrom purrr map reduce
#' @importFrom tidyr pivot_longer pivot_wider
## usethis namespace: end
NULL
29 changes: 29 additions & 0 deletions man/gimap-package.Rd

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41 changes: 38 additions & 3 deletions man/gimap_filter.Rd

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3 changes: 3 additions & 0 deletions man/qc_cdf.Rd

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24 changes: 22 additions & 2 deletions man/qc_constructs_countzero_bar.Rd

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3 changes: 2 additions & 1 deletion man/qc_cor_heatmap.Rd

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44 changes: 44 additions & 0 deletions man/qc_filter_plasmid.Rd

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10 changes: 8 additions & 2 deletions man/qc_filter_zerocounts.Rd

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31 changes: 28 additions & 3 deletions man/qc_plasmid_histogram.Rd

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3 changes: 2 additions & 1 deletion man/qc_sample_hist.Rd

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