plotStrandedCoverage: Plot strand-specific read coverage for a GRanges object

In RIPSeeker: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

Description

Plot read counts within fixed bin across the entire chromosome.

Usage

plotStrandedCoverage(gr, binSize = 1000, plotLegend = FALSE, ylim, ...)

Arguments

gr	GRanges object containing the alignments.
binSize	Integer indicate the size of the bin used to compute and plot the read counts.
plotLegend	Binary indcator. If TRUE, legend will be plotted on the top left the plot. Legend is expected to be the chromsome name and length, which must be available in the GRange object argument.
ylim	A two element scale on the y-axis, indicating the maximum read counts on the + and - strand to be plotted (e.g., ylim=c(-200, 200)).
...	Extra arguments passed to plotCoverage.

Details

Read count on + and - strand are displayed as red and blue bars on the positive and negative y-axis, respectively. The x-axis indicates the positions across the chromosmoe. The plot can be used to examine for each chromosome the overall alignment properties such as strand specificity (expected in non-strand-specific sequencing) and aggregation of reads.

Author(s)

Yue Li

References

P. Aboyoun, H. Pages and M. Lawrence (). GenomicRanges: Representation and manipulation of genomic intervals. R package version 1.8.9.

See Also

plotCoverage, plot, legend

Examples

# Retrieve system files
extdata.dir <- system.file("extdata", package="RIPSeeker") 

bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)

bamFiles <- grep("PRC2", bamFiles, value=TRUE)

alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")

alignGR <- as(alignGal, "GRanges")

alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))

binSize <- 1000

plotStrandedCoverage(gr=alignGRList$chrX, binSize=binSize,

		xlab="", ylab="", plotLegend=TRUE, box.lty=0, legend.cex=2 )

RIPSeeker documentation built on Oct. 31, 2019, 7:29 a.m.