fcros (version 1.6-6)

chrPlot: Plot a chromosome data

Description

This function generates a picture using a chromosome data.

Usage

chrPlot(chrData, thr = 0.05, deb = 100, fin = 1e10)

Value

This function generates a picture on the screen

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

Author

Doulaye Dembele [e-mail]

References

Dembele D, Analysis of high-throughput biological data using their rank values, Stat Meth Med Res, 2019, 28(8)2276-2291

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)