exomePeak的使用

R：http://www.bioconductor.org/packages/release/bioc/html/exomePeak.html

安装：# 看来作者更新的挺好

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("exomePeak", version = "3.8")

安装有问题……

用bioclite安装好了：

source("http://bioconductor.org/biocLite.R")

biocLite("exomePeak")

使用：

library('exomePeak')

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)

result = exomepeak(GENE_ANNO_GTF=GENE_ANNO_GTF, IP_BAM=IP_BAM, INPUT_BAM=INPUT_BAM,TREATED_IP_BAM=TREATED_IP_BAM, TREATED_INPUT_BAM=TREATED_INPUT_BAM)

UCSC_TABLE_NAME = "?" #如下：

gtf给的例子：

如果只需要找peaks：

result_OHT = exomepeak(GENOME = "mm10",UCSC_TABLE_NAME = "ensGene", IP_BAM=c(f1,f2), INPUT_BAM=c(f3,f4),EXPERIMENT_NAME = "exomePeak_OHT")

result_DMSO = exomepeak(GENOME = "mm10",UCSC_TABLE_NAME = "ensGene", IP_BAM=c(f5,f6), INPUT_BAM=c(f7,f8)，EXPERIMENT_NAME = "exomePeak_DMSO")

结果：

结果说明：http://www.bioconductor.org/packages/release/bioc/vignettes/exomePeak/inst/doc/exomePeak-Overview.pdf

主要看con_sig_diff_peaks igv-1-chr1 igv-2