chrSegment: Segmentation of a chromosome data

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

Description

This function allows to segment a chromosome data

Usage

chrSegment(chrData, nd = 10)

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

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

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)

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

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