Make package public

This is a breaking change. We remove the default argument for the
`get_gft()` function to remove dependence on the Kwan lab file system.
Now, a file path to a GTF must be provided.

Additionally, `perform_edger()` can now receive for the `gtf` argument
 either a GTF dataframe
object or a file path to a GTF.

Author: ofarrelle

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: kwanlibr
 Title: edgeR wrapper for simple differential expression analysis
-Version: 1.2.3
+Version: 1.3.0
 Authors@R: 
     c(
         person("Yaman", "Qalieh", , "yamanq@umich.edu", role = c("aut", "cre"),

R/core_edger_analyzer.R

@@ -37,17 +37,16 @@ VOLCANO_RED = '#d80303'
 #'
 #' get_gtf(gtf, verbose) returns the reference specified by
 #' the path gtf.
-#' @param gtf Absolute path to the reference. Default is the GENCODE annotation
-#' for mm10/GRCm38
+#' @param gtf Absolute path to the reference
 #' @param verbose Set to TRUE to print number of genes in the reference
 #' @return A dataframe of gene annotations with 3 columns: the ensembl
 #' `gene_id`, the `gene_type`, and `gene_name` (gene symbol)
 #' @export
 #' @examples
-#' get_gtf(gtf='/nfs/turbo/umms-kykwan/projects/reference/gtf/gencode.vM14.primary_assembly.ERCC.annotation.gtf')
+#' get_gtf(gtf='reference/gtf/gencode.vM14.primary_assembly.ERCC.annotation.gtf')
 
 get_gtf <- function(
-  gtf='/nfs/turbo/umms-kykwan/projects/reference/gtf/gencode.vM14.primary_assembly.annotation.gtf',
+  gtf,
   verbose=FALSE
 ) {
 
@@ -81,7 +80,7 @@ get_gtf <- function(
 #' refers to the batch of the sample. If NULL, no batch correction
 #' @param filePrefix Prefix to add to filenames (e.g. if they are in a different
 #'  directory). If NULL, search the current working directory
-#' @param gtf A dataframe of the reference genome, generated by `kwanlibr::get_gtf`
+#' @param gtf Either a dataframe of the reference genome generated by `kwanlibr::get_gtf`, or a path to the reference genome.
 #' @param saveName Filename to save edgeR tables under. Saves top 5k genes and
 #' all genes. If NULL, do not save tables.
 #' @return A dataframe of the edgeR analysis
@@ -104,8 +103,12 @@ perform_edger <- function(
   }
   filePrefix <- gsub("/+$", "", filePrefix)
 
-  if (class(gtf) == "NULL") {
-    gtf <- kwanlibr::get_gtf()
+  if (class(gtf) == "character") {
+    paste0("Getting GTF from ", gtf)
+    gtf <- kwanlibr::get_gtf(gtf)
+  }
+  else if (class(gtf) != "data.frame") {
+    stop("Provide a GTF with kwanlibr::get_gtf()")
   }
 
   if(class(batchCol) == "NULL"){

informal_tests/test_core_edger_analyzer.R

@@ -34,6 +34,8 @@ exp_samples = kwanlibr::label_control_samples(exp_samples, 'Condition', 'ctrl')
 # ===================
 # Test perform_edger
 # ===================
+
+# GTF object
 lrt = kwanlibr::perform_edger(
   exp_samples,
   filePrefix = config$paths$gene_counts_dir,
@@ -42,6 +44,23 @@ lrt = kwanlibr::perform_edger(
   saveName = paste0(config$paths$test_results_dump, 'edger_lrt')
 )
 
+# GTF file path
+lrt = kwanlibr::perform_edger(
+  exp_samples,
+  filePrefix = config$paths$gene_counts_dir,
+  idCol = 'Pool.Name',
+  gtf=config$paths$gtf,
+  saveName = paste0(config$paths$test_results_dump, 'edger_lrt')
+)
+
+# no GFT
+lrt = kwanlibr::perform_edger(
+  exp_samples,
+  filePrefix = config$paths$gene_counts_dir,
+  idCol = 'Pool.Name',
+  saveName = paste0(config$paths$test_results_dump, 'edger_lrt')
+)
+
 # ===================
 # Test make_volcano_dataframe
 # ===================