WebContainer for aCGH regions data and experimental metadata. cghRegions class is derived from eSet , and requires a matrix named regions as assayData member. Furthermore, columns named Chromosome, Start, End, Nclone, and Avedist are required as featureData … WebCGHregions takes as input array CGH data (log2-ratios) that have been segmented (i.e., split into chromosomal segments of similar log2-ratios) and called (i.e., a copy number assigned to each segment) on a per-sample basis and adjusts the segmentation so that break-points that are in similar locations across multiple samples are set to be in …
CGHregions: Dimension Reduction for Array CGH Data with …
WeboutputToCGHregions (ffoutput = NULL, directory = getwd (), output.dat = NULL, chrom.dat = NULL, pos.dat = NULL, probenames.dat = NULL) Arguments ffoutput The name of the … WebFinally, for other downstream analyses, such as running CGHregions, it might be useful to converttoacghCall object. > cgh <- makeCgh(copyNumbersCalled) > cgh cghCall (storageMode: lockedEnvironment) assayData: 33347 features, 1 samples element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, segmented … baterai huangmi f8 eleven
CGHregions: dimension reduction for array CGH data with …
Webplot.cghRegions Create a plot displaying chromosomes on the Y-axis and base pair position on the X-axis. A new region is displayed by a slight jump with respect to the previous region. Each region is displayed as a bi-colored segment, the lower and upper part of which correspond to WebNov 8, 2024 · CGHregionsfunction. The first four columns are the probe name, the chromosome, the position and the position. The last k columns are the calls for the k samples. Note This function does NOT check if the calls are meaningfull. particular, you probably do NOT want to use this function when pSegmenthas been called using … WebAn algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. This reduction of the data is performed such … tatra banka bratislava bic