fcros (version 1.6-6)

chrSegment: Segmentation of a chromosome data

Description

This function allows to segment a chromosome data

Usage

chrSegment(chrData, nd = 10)

Value

This function returns a data frame containing 6 information for each segment

idStart

The start position indexes associated with segments

idEnd

The End position indexes associated with segments

lBounds

The lower bound positions associated with segments

uBounds

The upper bound positions associated with segments

segL2R

The change values associated with segments

segProba

The probabilities associated with segments

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, ]

nd

The acceptable number of non-detected probes which can separate two significant probes in a segment. Default setting value is 10: nd = 10

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 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)

    # show first 10 segment results
    chrSeg[1:10,]