## ----eval=FALSE---------------------------------------------------------- # source("http://www.bioconductor.org/biocLite.R") # biocLite("ssviz") ## ----loadingPackage,message=FALSE---------------------------------------- library(ssviz) ## ----loaddata------------------------------------------------------------ data(ssviz) ## ----loading-bam,tidy=TRUE,warning=FALSE--------------------------------- bam.files<-dir(system.file("extdata", package="ssviz"), full=TRUE, patt="bam$") ctrlbam<-readBam(bam.files[1]) treatbam<-readBam(bam.files[2]) ## ----viewobject---------------------------------------------------------- ctrlbam ## ----gettingReadCounts,warning=FALSE------------------------------------- ctrl.count<-getCountMatrix(ctrlbam) treat.count<-getCountMatrix(treatbam) ## ----gettingReadCounts2,warning=FALSE------------------------------------ ctrl.count[1,] ## ----plotdistro1,tidy=TRUE,eval=FALSE------------------------------------ # plotDistro(list(ctrl.count), type="qwidth", samplenames=c("Control"), ncounts=counts[1]) ## ----plotdistro2,tidy=TRUE,eval=FALSE,warning=FALSE---------------------- # plotDistro(list(ctrl.count, treat.count), type="qwidth", samplenames=c("Control","Treatment"), ncounts=counts) ## ----regiondens,eval=FALSE----------------------------------------------- # region<-'chr1:3015526-3080526' # plotRegion(list(ctrl.count), region=region) ## ----pingpong,eval=FALSE------------------------------------------------- # pp.ctrl<-pingpong(pctrlbam.count) # plotPP(list(pp.ctrl), samplenames=c("Control")) ## ----ntfreq,eval=FALSE--------------------------------------------------- # pctrlbam.count<-getCountMatrix(pctrlbam) # freq.ctrl<-ntfreq(pctrlbam.count, ntlength=10) # plotFreq(freq.ctrl) ## ------------------------------------------------------------------------ sessionInfo()