xyplotLrrBaf: xyplot lattice function for RangedData and oligoSnpSet...

In SNPchip: Visualizations for copy number alterations

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

rd	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.

Details

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

Value

A trellis object.

Author(s)

R. Scharpf

See Also

xypanelBaf

Examples

  ## 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)

SNPchip documentation built on Oct. 31, 2019, 2:07 a.m.