CHipQC在PC环境成功运行

#SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller
#BT4741 BT474 ER Resistant Full-Media 1 reads/Chr18_BT474_ER_1.bam reads/Chr18_BT474_input.bam reads/Chr18_BT474_input.bam peaks/BT474_ER_1.bed.gz bed
#BT4742 BT474 ER Resistant Full-Media 2 reads/Chr18_BT474_ER_2.bam reads/Chr18_BT474_input.bam reads/Chr18_BT474_input.bam peaks/BT474_ER_2.bed.gz bed

setwd(‘C:\Users\Administrator\Desktop\diffbind\ALLHDNC\DiffBind_Vignette\’)

library(BiocParallel)###PC run request
register(SerialParam())

library(ChIPQC)
samples = read.csv(file.path(system.file(“extdata”, package=“ChIPQC”), “example_QCexperiment.csv”))
samples

samples = read.csv(“C:\Users\Administrator\Documents\R\win-library\4.0\ChIPQC\extdata\tamoxifenQC.csv”)
samples
exampleExp = ChIPQC(samples, annotation = “hg19”, chromosome = “chr18”)

chipObj <- ChIPQC(samples, annotation=“hg19”) ##成功！sucess!

getwd()

ChIPQC需要调用BiocParallel，windows用户可能报错，可以先运行一句：register(SerialParam())

Create ChIPQC report

ChIPQCreport(chipObj, reportName=“ChIP QC report: Nanog and Pou5f1”, reportFolder=“ChIPQCreport”)

####example2 failure
library(ChIPQC)
sample2=ChIPQCsample(“C:\Users\Administrator\Desktop\diffbind\ALLHDNC\DiffBind_Vignette\reads\Chr18_BT474_ER_1.bam”)
sample2 ##failure