xyplotLrrBaf {SNPchip} | R Documentation |
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.
xyplotLrrBaf(rd, object, frame, ...)
rd |
An instance of |
object |
A |
frame |
The genomic distance in basepairs to plot on either side
of the genomic interval in the |
... |
Additional arguments passed to the panel function. See details. |
The xypanelBaf
function is a panel function that does
the actual plotting of the genomic data.
A trellis
object.
R. Scharpf
## Not run: library(crlmm) library(SummarizedExperiment) library(VanillaICE) data(cnSetExample, package="crlmm") oligoSetList <- BafLrrSetList(cnSetExample[, 1]) oligoSet <- oligoSetList[[1]] cn <- copyNumber(oligoSet)/100 cn <- log2((2^cn)/2) gt <- calls(oligoSet)[,] ## simulate BAFs bf <- baf(oligoSet)[, ]/1000 gr <- GRanges(paste0("chr", chromosome(featureData(oligoSet))), IRanges(position(oligoSet), width=1)) cn <- as.matrix(cn) bf <- as.matrix(bf) dimnames(cn) <- dimnames(bf) <- list(featureNames(oligoSet), sampleNames(oligoSet)) se <- SnpArrayExperiment(cn=cn, baf=bf, rowRanges=gr, isSnp=rep(TRUE, length(gr))) fit <- hmm2(se) ##rd <- fit[sampleNames(fit)=="NA19007", ] rd <- as(segs(fit), "GRanges") ## 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)) ## End(Not run)