chrPlot2 {fcros}

Plot a chromosome segmentation results

Description

This function generates a picture. It uses a chromosome data and the output results of the segmentation function chrSegment().

Usage

chrPlot2(chrData, chrSeg, deb = 100, fin = 1e10)

Arguments

chrData

A chromosome data obtained from an output of the function dataSummary(): xinfo2 = dataSummary(af, xinfo, chromosomes, alpha)
idx = which(xinfo2$xinfo.s$Chromosome == "chr1")
chrData = xinfo2$xinfo.s[idx, ]

chrSeg

An output object of the function chrSegment(): chrSeg = chrSegment(chrData, nd = 10)

deb

This parameter allows to specify the start position of the chromosome region for plotting. It can be used for zooming. Negative value will lead to the plot of all chromosome data. deb = 100

fin

This parameter allows to specify the end position of the chromosome region for plot. It can be used for zooming. Negative value will lead to the plot of all chromosome data. thr = 1e7

Value

This function generates a picture on the screen

Author(s)

Doulaye Dembele [e-mail]

References

Dembele D, Analysis of high biological data using their rank values, Stat Methods Med Res, accepted for publication, 2018

Examples

    # load CGH data and info files
    data(cghData)
    rownames(cghData) <- cghData[,1];
    data(cghInfo)
    noms <- colnames(cghData)
    m <- length(noms)
    samp  <- noms[2:m]

    # associate statistics with probes in the dataset
    af <- pfcoMod(cghData, samp, log2.opt = 0, trim.opt = 0.25)

    chromosomes <- c(7:9)
    alpha <- 0.05

    # summarize results for each chromosome
    xinfo2 <- dataSummary(af, cghInfo, chromosomes, alpha)

    # focused on chromosome 7 data
    idx <- which(xinfo2$xinfo.s$Chromosome == "7")
    chrData <- xinfo2$xinfo.s[idx, ]

    # segment chromosome 7 data
    chrSeg <- chrSegment(chrData, nd = 15)

    # plot chromosome 7 results
    op <- par(mfrow = c(2,1))
    chrPlot(chrData, thr = alpha, deb =-1, fin = 3.5e7)
    chrPlot2(chrData, chrSeg, -1, fin = 3.5e7)
    par(op)