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Cghregions

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 https://cciwest.net

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

CGHregions: Dimension Reduction for Array CGH …

Category:Visualization of 68 regions created by CGHregions for 37 …

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Cghregions

CGHregions: Dimension Reduction for Array CGH Data with …

Web3.1 CGHregions [30] As mentioned before (Section 2), this method is designed to capture patterns such as those in Scenario V of Figure 1, and has therefore been considered a dimension reduction ... WebUsing multiple testing corrections suitable for these data, we provide statistical evidence for genomic differences on several clone regions between MSI+ and CIN+ tumors. The algorithm, named CGHregions, is available as an easy-to-use script in R.

Cghregions

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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 that little information ... WebDimension Reduction for Array CGH Data with Minimal Information Loss

WebJan 1, 2007 · CGHregions is also advantageous for cluster analysis of the called array CGH data (van Wieringen et al. 2006b). The use of regions, rather than clones, as input …

WebDOI: 10.18129/B9.bioc.CGHregions Dimension Reduction for Array CGH Data with Minimal Information Loss. Bioconductor version: Release (3.15) Dimension Reduction for Array CGH Data with Minimal Information Loss. Author: Sjoerd Vosse &amp; Mark van de Wiel . Maintainer: Sjoerd Vosse WebThe algorithm, named CGHregions, is available as an easy-to-use script in R. Keywords: Array CGH; Dimension reduction; Tumor profiles; Statistical testing; FDR.

WebIn the above, the directive will reference an actual container provided by the module, for the version you have chosen to load. An environment file in the module folder will also be bound. Note that although a container might provide custom commands, every container exposes unique exec, shell, run, and inspect aliases.

WebContainer for aCGH regions data and experimental metadata. cghRegions class is derived from eSet , and requires a matrix named regions as assayData member. Furthermore, … tatra banka bratislava pobočkyWebCGHregions 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 … baterai huawei cun l22WebNov 8, 2024 · CGHregions 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., … tatra banka dlzniciWebCGHregions 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 … baterai ht hyteraWebMar 8, 2024 · CGHregions home page: release version, devel version. Number of downloads for software package CGHregions, year by year, from 2024 back to 2009 … baterai htcWebCGHregions_1.57.0.zip: macOS Binary (x86_64) CGHregions_1.57.0.tgz: macOS Binary (arm64) CGHregions_1.57.0.tgz: Source Repository: git clone … baterai ht yaesu vx 6WebThe algorithm, named CGHregions, is available as an easy-to-use script in R. Keywords: Array CGH; Dimension reduction; Tumor profiles; Statistical testing; FDR. Introduction baterai huawei hb434666rbc