Replace Diff_analysis.R added new binomtest mean

scripts/Diff_analysis.R

@@ -7,7 +7,6 @@
 # import
 library(DESeq2)
 
-
 # Functions
 run_analysis <- function(file_name) {
   data <- read.table(file_name, row.names = 1, header=TRUE)
@@ -29,8 +28,8 @@ run_analysis <- function(file_name) {
   
   # do glm test
   dds = nbinomWaldTest(dds)
-  res = results(dds)
-  write.table(res, col.names=NA, row.names=T, file =paste(file_name, ".tsv"), sep ="\t")
+  res = results(dds, lfcThreshold=1, altHypothesis="greaterAbs")
+  write.table(res, col.names=NA, row.names=T, file =paste(file_name,".tsv", collapse="", sep=""), sep ="\t")
 }