dataSummary: Summarization of the detection results for a list of...

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

Description

From an outpout object of the function fcrosMod() or pfcoMod(), the chromosomes information object, the list of chromosomes and a threshold, this function creates two objects containing ordered chromosome data and summary results.

Usage

dataSummary(af, xinfo, chromosomes = c(1:22,"X","Y"), alpha = 0.05)

Arguments

af	An output object of the function fcrosMod() or pfcoMod(): af = fcrosMod(xdata, samp, log2.opt, trim.opt) af = pfcoMod(xdata, samp, log2.opt, trim.opt)
xinfo	A data frame containing chromosomes information (probe name, gene symbol, chromosome index, start position, end position and the cytoband). These information should appear with the labels ProbeName, GeneSymbol, Chromosome, Start, End, Cytoband. Additional information may be used. Only labels Chromosome, Start and End are mandotory.
chromosomes	A list of chromosomes. Default setting is a list with all chromosomes: chromosomes = (1:22,"X","Y")
alpha	A threshold allowing to select significant probes based on probabilities. Default setting is 0.05 (5% of error) thr = 0.05

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)

    # display the number of significant probes for each chromosome
    xinfo2$chrSumm

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