1d:T784,# Segmentation of a chromosome data This function allows to segment a chromosome data ```r 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$xinfo.s[idx, ] - `nd`: The acceptable number of non-detected probes which can separate two significant probes in a segment. Default setting value is 10: `nd` = 10 ## Returns This function returns a data frame containing 6 information for each segment - **idStart**: The start position indexes associated with segments - **idEnd**: The End position indexes associated with segments - **lBounds**: The lower bound positions associated with segments - **uBounds**: The upper bound positions associated with segments - **segL2R**: The change values associated with segments - **segProba**: The probabilities associated with segments ## Author(s) Doulaye Dembele doulaye@igbmc.fr ## References Dembele D, Analysis of high biological data using their rank values, Stat Methods Med Res, accepted for publication, 2018 ## Examples ```r # load CGH data and info files data(cghData) rownames(cghData) <- cghData[,1] data(cghInfo) noms <- colnames(cghData) m <- length(noms) samp <- noms[2:m] # associate statistics with probes in the dataset af <- pfcoMod(cghData, samp, log2.opt = 0, trim.opt = 0.25) chromosomes = c(7:9) alpha <- 0.05 # summarize results for each chromosome xinfo2 <- dataSummary(af, cghInfo, chromosomes, alpha) # focused on chromosome 7 data idx <- which(xinfo2$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,] ```

chrSegment.rd function