### R code from vignette source 'RIPSeekerData.Rnw' ################################################### ### code chunk number 1: PRC2 ################################################### library(RIPSeeker) extdata.dir <- system.file("extdata", package="RIPSeekerData") bamFiles <- list.files(extdata.dir, "\\.bam$", recursive=TRUE, full.names=TRUE) bamFiles.PRC2 <- grep("PRC2/", bamFiles, value=TRUE) # import, process, and convert BAM data to GappedAlignments object # using function combineAlignGals # PRC2 PRC2.rip <- grep(pattern="SRR039214", bamFiles.PRC2, value=TRUE, invert=TRUE) PRC2.rip.biorep1 <- PRC2.rip[grep(pattern="SRR039213", PRC2.rip, invert=TRUE)] PRC2.rip.biorep2 <- PRC2.rip[grep(pattern="SRR039213", PRC2.rip, invert=FALSE)] PRC2.ctl <- grep(pattern="SRR039214", bamFiles, value=TRUE, invert=FALSE) ripGal.PRC2.rip.biorep1 <- combineAlignGals(PRC2.rip.biorep1, reverseComplement=TRUE, genomeBuild="mm9") ripGal.PRC2.rip.biorep2 <- combineAlignGals(PRC2.rip.biorep2, reverseComplement=TRUE, genomeBuild="mm9") ripGal.PRC2.ctl <- combineAlignGals(PRC2.ctl, reverseComplement=TRUE, genomeBuild="mm9") ripGal.PRC2.rip.biorep1 ripGal.PRC2.rip.biorep2 ripGal.PRC2.ctl ################################################### ### code chunk number 2: CCNT1 ################################################### library(RIPSeeker) extdata.dir <- system.file("extdata", package="RIPSeekerData") bamFiles <- list.files(extdata.dir, "\\.bam$", recursive=TRUE, full.names=TRUE) bamFiles.CCNT1 <- grep("CCNT1/", bamFiles, value=TRUE) # import, process, and convert BAM data to GappedAlignments object # using function combineAlignGals CCNT1.rip <- grep(pattern="humanCCNT1", bamFiles.CCNT1, value=TRUE, invert=TRUE) CCNT1.ctl <- grep(pattern="humanGFP", bamFiles.CCNT1, value=TRUE, invert=TRUE) ripGal.CCNT1.rip <- combineAlignGals(CCNT1.rip, reverseComplement=TRUE, genomeBuild="hg19") ripGal.CCNT1.ctl <- combineAlignGals(CCNT1.ctl, reverseComplement=TRUE, genomeBuild="hg19") ripGal.CCNT1.rip ripGal.CCNT1.ctl ################################################### ### code chunk number 3: sessi ################################################### sessionInfo()