set default FC threshold to 1.5 instead of 2

SnakeChunks · Oct 17, 2018 · e0a5051 · e0a5051
1 parent 6c5858f
commit e0a5051
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/scripts/RSnakeChunks/R/deg_table_postprocessing.R b/scripts/RSnakeChunks/R/deg_table_postprocessing.R
@@ -26,7 +26,7 @@
 #' @param sort.column="none" Column to sort the result.
 #' Supported: c("none", "mean", "log2FC", "pvalue", "padj").
 #'
-#' @param thresholds=c(padj = 0.05, FC = 2)
+#' @param thresholds=c(padj = 0.05, FC = 1.5)
 #'
 #' Thresholds on some specific scores, used for display purpose, and to
 #' add some columns to the result table, indicating if the gene passes the
@@ -62,7 +62,7 @@
 DEGtablePostprocessing <- function(deg.table,
                                table.name="DEG_table",
                                sort.column = "none",
-                               thresholds = c(padj = 0.05, FC = 2),
+                               thresholds = c(padj = 0.05, FC = 1.5),
                                round.digits = 3,
                                dir.figures = NULL,
                                verbose = 0) {

diff --git a/scripts/RSnakeChunks/R/deseq2_analysis.R b/scripts/RSnakeChunks/R/deseq2_analysis.R
@@ -8,7 +8,7 @@
 #' @param condition a vector with the condition associated to each sample. The length of this vector must equal the number of columns of the count table.
 #' @param ref.condition=NULL reference condition for the differential analysis
 #' @param comparison.prefix a string with the prefix for output files
-#' @param thresholds=c(padj=0.05,FC=2) thresholds on adjusted p-value (padj) and fold change (FC).
+#' @param thresholds=c(padj=0.05,FC=1.5) thresholds on adjusted p-value (padj) and fold change (FC).
 #' The result table will include columns indicating which feature pass these thresholds.
 #' See DEGtablePostprocessing() for supported thresholds.
 #' @param title=comparison.prefix main title for the plots
@@ -19,7 +19,7 @@
 deseq2.analysis <- function(counts,
                             condition,
                             ref.condition = NULL,
-                            thresholds = c(padj = 0.05, FC = 2),
+                            thresholds = c(padj = 0.05, FC = 1.5),
                             comparison.prefix,
                             title = comparison.prefix,
                             dir.figures = NULL,

diff --git a/scripts/RSnakeChunks/R/edger_analysis.R b/scripts/RSnakeChunks/R/edger_analysis.R
@@ -12,7 +12,7 @@
 #' @param title=comparison.prefix main title for the plots
 #' @param dir.figures=NULL optional directory to save figures
 #' @param norm.method="TMM" normalisation method. This parameter strongly affects the results! See edgeR documentation for a list of supported methods
-#' @param thresholds=c(padj=0.05,FC=2) thresholds on adjusted p-value (padj) and fold change (FC).
+#' @param thresholds=c(padj=0.05,FC=1.5) thresholds on adjusted p-value (padj) and fold change (FC).
 #' The result table will include columns indicating which feature pass these thresholds.
 #' See DEGtablePostprocessing() for supported thresholds.
 #' @param verbose=0 level of verbosity
@@ -23,7 +23,7 @@ edger.analysis <- function(counts,
                            test.condition = 1,# first condition for edegR::exactTest()
                            ref.condition = 2, # second condition for edgeR::exactTest()
                            norm.method = "TMM",
-                           thresholds = c(padj = 0.05, FC = 2),
+                           thresholds = c(padj = 0.05, FC = 1.5),
                            comparison.prefix,
                            title = paste(sep = "_", norm.method, comparison.prefix),
                            dir.figures = NULL,