xyplotLrrBaf: xyplot lattice function for RangedData and oligoSnpSet objects

Description

For each genomic interval in the ranged data, a plot of the log R ratios and B allele frequencies stored in the oligoSnpSet are plotted.

Usage

xyplotLrrBaf(rd, object, frame, ...)

Arguments

An instance of RangedDataCNV or GRanges.

object

A oligoSnpSet or BeadStudioSet object with assayData elements for log R ratios and B allele frequencies.

frame

The genomic distance in basepairs to plot on either side of the genomic interval in the rd object.

...

Additional arguments passed to the panel function. See details.

Value

A trellis object.

Details

The xypanelBaf function is a panel function that does the actual plotting of the genomic data.

Examples

Run this code

library(crlmm)
library(SummarizedExperiment)
library(VanillaICE)
data(cnSetExample, package="crlmm")
oligoSetList <- BafLrrSetList(cnSetExample)
fit <- hmm(oligoSetList, p.hom=0)[[1]]
rd <- fit[sampleNames(fit)=="NA19007", ]
## We're interested in this range
range <- GRanges("chr8", IRanges(3.7e6, 5.9e6), sample="NA19007")
index <- subjectHits(findOverlaps(range, rd))
xyplotLrrBaf(rd[index, ], oligoSetList[[1]], frame=1e6,
	     panel=xypanelBaf, cex=0.2,
	     scales=list(x=list(relation="free"),
	     y=list(alternating=1,
	     at=c(-1, 0, log2(3/2), log2(4/2)),
	     labels=expression(-1, 0, log[2](3/2), log[2](4/2)))),
	     par.strip.text=list(cex=0.7),
	     ylim=c(-3,1),
	     col.hom="grey50",
	     col.het="grey50",
	     col.np="grey20",
	     xlab="physical position (Mb)",
	     ylab=expression(log[2]("R ratios")),
	     key=list(text=list(c(expression(log[2]("R ratios")), expression("B allele freqencies")),
		      col=c("grey", "blue")), columns=2))

## Or, plot each range of the GRanges instance in a separate panel
xyplotLrrBaf(rd, oligoSetList[[1]], frame=1e6,
	     panel=xypanelBaf, cex=0.2,
	     scales=list(x=list(relation="free"),
	     y=list(alternating=1,
	     at=c(-1, 0, log2(3/2), log2(4/2)),
	     labels=expression(-1, 0, log[2](3/2), log[2](4/2)))),
	     par.strip.text=list(cex=0.7),
	     ylim=c(-3,1),
	     col.hom="grey50",
	     col.het="grey50",
	     col.np="grey20",
	     xlab="physical position (Mb)",
	     ylab=expression(log[2]("R ratios")),
	     key=list(text=list(c(expression(log[2]("R ratios")), expression("B allele freqencies")),
		      col=c("grey", "blue")), columns=2))