setwd('/Volumes/BB_Backup_3/BD_aging_project/2018-09_revision_analyses/TE_chromatin/RepeatMasker/H3K4me3_TEs')
setwd('/Volumes/BB_Backup_3/BD_aging_project/2018-09_revision_analyses/TE_chromatin/RepeatMasker/H3K4me3_TEs')
my.liver.data <- read.table("../Diffbind/2018-09-12_Liver_H3K4me3_aging_Repeats_DiffBind_normalized_counts.txt",header=T,sep="\t")
head(my.liver.data)
my.liver <- my.liver.data[,4:9]
rownames(my.liver) <- paste(my.liver.data[,1],my.liver.data[,2],my.liver.data[,3],sep="-")
colnames(my.liver) <- c("3m1","3m2","12m1","12m2","29m1","29m2")
my.tissue <- "Liver"
my.matrix <- my.liver
my.annot <- "../Peaks_intersecting_repeats/Liver_H3K4me3_Repeatmasker_mm9_100bp_extend.bed"
reps.3=2
reps.12=2
reps.29=2
my.peak.annot <- read.csv(my.annot,header=F,sep="\t")
head(my.peak.annot)
my.peak.annot <- read.csv(my.annot,header=F,sep="\t")
my.peak.annot$CoordName <- paste(my.peak.annot[,1],my.peak.annot[,2],my.peak.annot[,3],sep="-")
my.peak.annot$Element <- paste(my.peak.annot[,4],my.peak.annot[,1],my.peak.annot[,2],my.peak.annot[,3],sep="-")
my.peak.annot$Family <- my.peak.annot[,4]
head(my.peak.annot)
my.matrix$CoordName <- rownames(my.matrix)
head(my.matrix)
my.matrix$CoordName <- paste("chr",rownames(my.matrix),sep="")
my.matrix$CoordName
