### R code from vignette source 'fCCAC.Rnw' ################################################### ### code chunk number 1: style ################################################### BiocStyle::latex() ################################################### ### code chunk number 2: setup ################################################### options(width=200) options(continue=" ") options(prompt="R> ") ################################################### ### code chunk number 3: fCCACexample ################################################### options(width=60); if (.Platform$OS.type == "windows") { print("...rtracklayer is unable to read bigWig format files in Windows...") } if (.Platform$OS.type == "unix") { ## hg19. chr21:40000000-48129895 H3K4me3 data from Bertero et al. (2015) owd <- setwd(tempdir()); library(fCCAC) bigwig1 <- "chr21_H3K4me3_1.bw" bigwig2 <- "chr21_H3K4me3_2.bw" bigwig3 <- "chr21_H3K4me3_3.bw" peakFile <- "chr21_merged_ACT_K4.bed" labels <- c( "H3K4me3", "H3K4me3","H3K4me3" ) r1 <- system.file("extdata", bigwig1, package="fCCAC",mustWork = TRUE) r2 <- system.file("extdata", bigwig2, package="fCCAC",mustWork = TRUE) r3 <- system.file("extdata", bigwig3, package="fCCAC",mustWork = TRUE) r4 <- system.file("extdata", peakFile, package="fCCAC",mustWork = TRUE) ti <- "H3K4me3 peaks (chr21)" fc <- fccac(bar=NULL, main=ti, peaks=r4, bigwigs=c(r1,r2,r3), labels=labels, splines=15, nbins=100, ncan=15) head(fc) setwd(owd) } ################################################### ### code chunk number 4: heatmapPlot ################################################### options(width=60) if (.Platform$OS.type == "windows") { print("...rtracklayer is unable to read bigWig format files in Windows...") } if (.Platform$OS.type == "unix" ){ heatmapfCCAC(fc) } ################################################### ### code chunk number 5: sessionInfo ################################################### sessionInfo()