# Plot a chromosome segmentation results This function generates a picture. It uses a chromosome data and the output results of the segmentation function chrSegment(). ```r chrPlot2(chrData, chrSeg, deb = 100, fin = 1e10) ``` ## 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$xinfo.s[idx, ] - `chrSeg`: An output object of the function chrSegment(): `chrSeg` = chrSegment(chrData, nd = 10) - `deb`: This parameter allows to specify the start position of the chromosome region for plotting. It can be used for zooming. Negative value will lead to the plot of all chromosome data. `deb` = 100 - `fin`: This parameter allows to specify the end position of the chromosome region for plot. It can be used for zooming. Negative value will lead to the plot of all chromosome data. `thr` = 1e7 ## Returns This function generates a picture on the screen ## Author(s) Doulaye Dembele doulaye@igbmc.fr ## References Dembele D, Analysis of high biological data using their rank values, Stat Methods Med Res, accepted for publication, 2018 ## Examples ```r # load CGH data and info files data(cghData) rownames(cghData) <- cghData[,1]; data(cghInfo) noms <- colnames(cghData) m <- length(noms) samp <- noms[2:m] # associate statistics with probes in the dataset af <- pfcoMod(cghData, samp, log2.opt = 0, trim.opt = 0.25) chromosomes <- c(7:9) alpha <- 0.05 # summarize results for each chromosome xinfo2 <- dataSummary(af, cghInfo, chromosomes, alpha) # focused on chromosome 7 data idx <- which(xinfo2$xinfo.s$Chromosome == "7") chrData <- xinfo2$xinfo.s[idx, ] # segment chromosome 7 data chrSeg <- chrSegment(chrData, nd = 15) # plot chromosome 7 results op <- par(mfrow = c(2,1)) chrPlot(chrData, thr = alpha, deb =-1, fin = 3.5e7) chrPlot2(chrData, chrSeg, -1, fin = 3.5e7) par(op) ```

chrPlot2.rd function