github：https://github.com/compgenomics/MeTDiff
# 安装：
library("devtools")
install_github("compgenomics/MeTDiff")
安装成功
# 使用：
library(MeTDiff)
GENE_ANNO_GTF="gencode.vm19.GRCm38.all.ano.gtf"
f1="R18060088-QMJ-Library-4-OHT-IP1_combined_R.bam"
f2="R18060088-QMJ-Library-4-OHT-IP2_combined_R.bam"
IP_BAM=c(f1,f2)
f3="OHT1.sorted.bam"
f4="OHT2.sorted.bam"
INPUT_BAM=c(f3,f4)
f5="R18060088-QMJ-Library-DMSO-IP1_combined_R.bam"
f6="R18060088-QMJ-Library-DMSO-IP2_combined_R.bam"
TREATED_IP_BAM=c(f5,f6)
f7="DMSO1.sorted.bam"
f8="DMSO2.sorted.bam"
TREATED_INPUT_BAM=c(f7,f8)
metdiff(GENE_ANNO_GTF=gtf,IP_BAM = IP_BAM,INPUT_BAM = INPUT_BAM,TREATED_IP_BAM = TREATED_IP_BAM,TREATED_INPUT_BAM=TREATED_INPUT_BAM,EXPERIMENT_NAME="example")
和exomepeak简直一模一样！
