## ----para, echo = FALSE, results='hide'--------------------------------------- BiocStyle::markdown() knitr::opts_chunk$set(dev="png",fig.show="hold", fig.width=8,fig.height=4.5,fig.align="center", message=FALSE,collapse=TRUE) set.seed(1) ## ----library------------------------------------------------------------------ library(gcapc) ## ----data--------------------------------------------------------------------- bam <- system.file("extdata", "chipseq.bam", package="gcapc") ## ----rc5end------------------------------------------------------------------- cov <- read5endCoverage(bam) cov ## ----bdwidth1----------------------------------------------------------------- bdw <- bindWidth(cov, range=c(50L,300L), step=10L) bdw ## ----gcbias------------------------------------------------------------------- layout(matrix(1:2,1,2)) gcb <- gcEffects(cov, bdw, sampling=c(0.25,1), plot=TRUE, model='poisson') ## ----gcapc, results='hide'---------------------------------------------------- layout(matrix(1:2,1,2)) peaks <- gcapcPeaks(cov, gcb, bdw, plot=TRUE, permute=100L) peaks <- gcapcPeaks(cov, gcb, bdw, plot=TRUE, permute=50L) ## ----gcapcpeaks--------------------------------------------------------------- peaks ## ----refine, results='hide', fig.width=4.5------------------------------------ newpeaks <- refinePeaks(cov, gcb, bdw, peaks=peaks, permute=50L) plot(newpeaks$es,newpeaks$newes,xlab='old score',ylab='new score') ## ----refinepeaks-------------------------------------------------------------- newpeaks