inst/doc/fCCAC.R

In fCCAC: functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

### R code from vignette source 'fCCAC.Rnw'

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### code chunk number 1: style
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BiocStyle::latex()


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### code chunk number 2: setup
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options(width=200)
options(continue=" ")
options(prompt="R> ")


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### code chunk number 3: fCCACexample
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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)

}



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### code chunk number 4: heatmapPlot
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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) }



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### code chunk number 5: sessionInfo
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sessionInfo()