I am working on ChipSeq data of histone marks. I am using Diffbind package. I have 8 samples in 2 groups each. I am trying to see differential peak enrichment in these two groups. I have used this to read one file at a time. How can I club 4 samples so that I can do a group comparison?
bedJ <- as.data.frame(read.table("CEMT_178.H3K27ac-J.bed",header = FALSE, sep="t",stringsAsFactors=FALSE, quote=""))