chrPlot: Plot a chromosome data

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

Description

This function generates a picture using a chromosome data.

Usage

chrPlot(chrData, thr = 0.05, 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, ]
thr	The probability threshold leading to the selection of the significant probes: thr = 0.05
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
    af <- fcrosMod(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, ]

    # Plot chromosome 7 data
    chrPlot(chrData, thr = alpha)

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