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Protocols

cghMCR specifications

Information


Unique identifier OMICS_00710
Name cghMCR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.18.0
Stability Stable
Requirements
limma, methods, DNAcopy, stats4, CNTools, BiocGenerics(>=0.1.6)
Maintained Yes

Versioning


No version available

Documentation


cghMCR citations

 (16)
library_books

A validation and extended description of the Lund taxonomy for urothelial carcinoma using the TCGA cohort

2018
Sci Rep
PMCID: 5829240
PMID: 29487377
DOI: 10.1038/s41598-018-22126-x

[…] ist the determination of the cutoffs. Used cutoffs for the samples are given in the Supplementary Table . The frequently altered regions in the cohort were determined using the R packages CNTools and cghMCR. Losses seen in more than 20%, and gains in more than 25% of the samples were included for further analyses (Supplementary Fig.  and Supplementary Table ). After determining the frequently alte […]

library_books

Genomic characterization of tobacco/nut chewing HPV negative early stage tongue tumors identify MMP10 as a candidate to predict metastases

2017
Oral Oncol
PMCID: 5628952
PMID: 28939077
DOI: 10.1016/j.oraloncology.2017.08.003

[…] We used Control-FREEC and cghMCR package to identify genomic regions harboring statistically significant copy number gains and losses relative to normal tissues. 440 amplified and 2275 deleted regions were identified across 23 […]

library_books

Microarray analysis of copy number variations and gene expression profiles in prostate cancer

2017
PMCID: 5515741
PMID: 28700469
DOI: 10.1097/MD.0000000000007264

[…] Raw aCGH data were preprocessed using the package cghMCR in R (version 1.34.0, http://www.bioconductor.org/packages/release/bioc/html/cghMCR.html).[,] The method “minimum” in the package was used for background correction, and this method meant that […]

library_books

Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis

2017
PMCID: 5588164
PMID: 28928828
DOI: 10.3892/ol.2017.6519

[…] p://www.Bioconductor.org/packages/release/bioc/html/crlmm.html) () in Bioconductor package version 1.0.2. Then, genes with copy number gains/losses were additionally screened using the DNAcopy () and cghMCR package (http://www.bioconductor.org/packages/2.4/bioc/html/cghMCR.html). Genes with copy number gains/losses (0.2 for gain, −0.2 for loss) in >30% samples was the threshold value for the DNAco […]

library_books

An evaluation of copy number variation detection tools for cancer using whole exome sequencing data

2017
BMC Bioinformatics
PMCID: 5452530
PMID: 28569140
DOI: 10.1186/s12859-017-1705-x

[…] For the gene-based comparison, we first annotated the detected CNV segments in the benchmark and samples for both real data and simulated data. We used “cghMCR” R package from Bioconductor [] to identify CNV genes using Refseq gene identifications. The average of the CNV values of the overlapping CNV segments for each gene is used as the gene CNV valu […]

library_books

Survival differences of CIMP subtypes integrated with CNA information in human breast cancer

2017
Oncotarget
PMCID: 5564726
PMID: 28415743
DOI: 10.18632/oncotarget.16178

[…] segment information into a reduced segment matrix (segments as rows and samples as columns), enabling a convenient calculation of the CNA frequency of regions in all samples. Lastly, the R function “cghMCR” (version 1.26.0) converted the matrix of regions into gene copy number profile and calculated their frequencies of CNA in all samples. We found there were apparently more CN gain than CN loss […]

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