MeTDiff的使用

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！

ref：exomePeak的使用 - 简书