Package: cnvGSA 1.49.0
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:
cnvGSA_1.49.0.tar.gz
cnvGSA_1.49.0.zip(r-4.5)cnvGSA_1.49.0.zip(r-4.4)cnvGSA_1.49.0.zip(r-4.3)
cnvGSA_1.49.0.tgz(r-4.4-any)cnvGSA_1.49.0.tgz(r-4.3-any)
cnvGSA_1.49.0.tar.gz(r-4.5-noble)cnvGSA_1.49.0.tar.gz(r-4.4-noble)
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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')) |
On BioConductor:cnvGSA-1.49.0(bioc 3.20)cnvGSA-1.48.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:82dcad7978
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.tabledoParallelforeachGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesiteratorsjsonlitemimeopensslprofileModelR6S4VectorssplitstackshapesysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gene-set Analysis of (Rare) Copy Number Variants | cnvGSA-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 |
