Merge branch 'master' of gitlab.pasteur.fr:hub/chipuanar

inst/Report_ChIPuanaR.Rmd

@@ -20,10 +20,10 @@ Site....
 # Package
 library(knitr)
 library(kableExtra)
-library(ChIPuana)
+library(ChIPuanaR)
 
 ### INPUTS
-source("../chipuana_rtest/config.R")
+source("config.R")
 data <- read.table(file = file, header=T)
 counts <- as.matrix(data[,-c(1:6)])
 rownames(counts) <- data[,1]
@@ -69,7 +69,7 @@ if (method=="Limma") {
 
 # Export result table
 for (name in names(resAnDif$results)){
-  write.table(resAnDif$results[name], file=paste0(name,"_resAnDif.txt"), sep="\t", row.names=FALSE, dec=".", quote=FALSE)
+  write.table(resAnDif$results[name], file=paste0(name,"_resAnDif.txt"), sep="\t", row.names=TRUE, dec=".", quote=FALSE)
 }
 ```
 
@@ -283,7 +283,7 @@ Parameter values used for this analysis are:
 - Replicates: `r Replicates`
 - Method: `r method`
 - Normalisation: `r ifelse(is.null(spikes),normalisation,"Spike-in")`
-- Spikes: `r ifelse(is.null(batch),"NULL",spikes)`
+- Spikes: `r ifelse(is.null(spikes),"NULL",spikes)`
 - batch: `r ifelse(is.null(batch),"NULL",batch)`
 - alpha: `r alpha`
 - pAdjustMethod: `r pAdjustMethod`