chrPlot2: Plot a chromosome segmentation results

In fcros: A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

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)

fcros documentation built on May 31, 2019, 5:03 p.m.