Package: cnvGSA 1.51.0

Joseph Lugo

cnvGSA: Gene Set Analysis of (Rare) Copy Number Variants

This package is intended to facilitate gene-set association with rare CNVs in case-control studies.

Authors:Daniele Merico <[email protected]>, Robert Ziman <[email protected]>; packaged by Joseph Lugo <[email protected]>

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cnvGSA.pdf |cnvGSA.html✨
cnvGSA/json (API)

# Install 'cnvGSA' in R:
install.packages('cnvGSA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:cnvGSA-1.51.0(bioc 3.21)cnvGSA-1.50.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

multiplecomparison

3.30 score 3 scripts 255 downloads 22 exports 26 dependencies

Last updated 2 months agofrom:66054b1916. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:cnvData.lscnvData.ls<-cnvGSAgsTablescnvGSAInCnvGSAInputcnvGSAlogRegTestCnvGSAOutputconfig.lsconfig.ls<-f.enrFilesf.makeVizf.readConfiggeneID.lsgeneID.ls<-gsData.lsgsData.ls<-gsTables.lsparams.lsparams.ls<-phData.lsphData.ls<-res.ls

Dependencies:askpassBiocGenericsbrglmcodetoolscurldata.tabledoParallelforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesiteratorsjsonlitemimeopensslprofileModelR6S4VectorssplitstackshapesysUCSC.utilsXVectorzlibbioc

cnvGSA - Gene-Set Analysis of Rare Copy Number Variants

Rendered fromcnvGSA-vignette.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2015-04-13
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Gene-set Analysis of (Rare) Copy Number VariantscnvGSA-package cnvGSA
Creates the gene-set tables for each gene-set.cnvGSAgsTables
Creating the input S4 object needed to run the script.cnvGSAIn
Class '"CnvGSAInput"'cnvData.ls cnvData.ls,CnvGSAInput-method cnvData.ls<- cnvData.ls<-,CnvGSAInput-method CnvGSAInput CnvGSAInput-class config.ls config.ls,CnvGSAInput-method config.ls<- config.ls<-,CnvGSAInput-method geneID.ls geneID.ls,CnvGSAInput-method geneID.ls<- geneID.ls<-,CnvGSAInput-method gsData.ls gsData.ls,CnvGSAInput-method gsData.ls<- gsData.ls<-,CnvGSAInput-method params.ls params.ls,CnvGSAInput-method params.ls<- params.ls<-,CnvGSAInput-method phData.ls phData.ls,CnvGSAInput-method phData.ls<- phData.ls<-,CnvGSAInput-method
Performing the logistic regression tests on the CNV data.cnvGSAlogRegTest
Class '"CnvGSAOutput"'CnvGSAOutput CnvGSAOutput-class gsData.ls,CnvGSAOutput-method gsTables.ls gsTables.ls,CnvGSAOutput-method phData.ls,CnvGSAOutput-method res.ls res.ls,CnvGSAOutput-method
Prepares the files for the enrichment maps.f.enrFiles
Creates the plots from the CnvGSAOutput data.f.makeViz
Reading in the config file.f.readConfig