CGHregions specifications

Information


Unique identifier OMICS_02058
Name CGHregions
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.39.0
Stability Beta
Requirements
methods, Biobase, R(>=2.0.0), CGHbase
Maintained Yes

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Documentation


Maintainer


  • person_outline Mark van de Wiel <>

Publication for CGHregions

CGHregions in publications

 (8)
PMCID: 5608257
PMID: 28165479
DOI: 10.1038/nm.4279

[…] or absence of the mutations within each sample. for the cn data the levels of alteration were categorized as homozygous deletion, loss, unchanged, gain and amplification. the bioconductor package cghregions was used for dimension reduction of the cn alteration matrix, in order minimize the weight of large alterations, and the resulting matrix was used as input for phangorn., representation […]

PMCID: 5342020
PMID: 27729614
DOI: 10.18632/oncotarget.12510

[…] median absolute deviation (mad) values below 0.4. array-cgh data is deposited in ncbi's gene expression omnibus (geo accession number gse75500)., dimension reduction was achieved by application of “cghregions” (version 1.22.0; setting: averror: 0.015) [] and resulted in 808 cna regions. these regions were subsequently used for two-group comparisons of stage ii versus iii and relapse versus […]

PMCID: 5083185
PMID: 27491809
DOI: 10.1038/modpathol.2016.134

[…] considered lost, modal copy number ≥ ploidy considered gained and modal copy number ≥ ploidy considered amplified. for each case, dimension reduction was performed using the bioconductor package cghregions to generate a matrix of collapsed copy number regions. oncoscan array data have been deposited to the ncbi gene expression omnibus under the accession gse79052., the cancer cell fraction […]

PMCID: 4873174
PMID: 27195705
DOI: 10.1371/journal.pone.0155840

[…] minimum number of 10 consecutive probes. the segmentation process was carried out using the dnacopy bioconductor package []. bioconductor´s cghcall package was employed for determining the step, and cghregions and cghtest packages[] were used to estimate genomic regions and false discovery rate, respectively., microarray and sequencing data have been deposited in geo and sra, under the following […]

PMCID: 4534696
PMID: 26288838
DOI: 10.1016/j.ebiom.2015.06.022

[…] estimates of the tumors and matched blood samples. for tumors with no matching blood sample, sex-matched pooled baselines from all blood samples were used to calculate log2-r ratios. cghcall () and cghregions () implementing the dnacopy segmentation algorithm were used to create a reduced segment matrix containing five copy number levels. all parameters used for copy number segmentations […]


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CGHregions institution(s)
Department of Pathology and Department of Biostatistics (KEB), VU University Medical Center, Amsterdam, Netherlands; Department of Mathematics, Vrije Universiteit, Amsterdam, Netherlands
CGHregions funding source(s)
Partly supported by the Center for Medical Systems Biology (CMSB) es tablished by the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research (NGI/NWO).

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