fcros (version 1.6.1)

chrSegment: Segmentation of a chromosome data

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

References

Dembele D, Analysis of high biological data using their rank values, Stat Methods Med Res, accepted for publication, 2018

Examples

# NOT RUN {
    # 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,]
# }