Package: cnvGSA 1.57.0
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_1.57.0.tar.gz
cnvGSA_1.57.0.zip(r-4.7)cnvGSA_1.57.0.zip(r-4.6)cnvGSA_1.57.0.zip(r-4.5)
cnvGSA_1.57.0.tgz(r-4.6-any)cnvGSA_1.57.0.tgz(r-4.5-any)
cnvGSA_1.57.0.tar.gz(r-4.7-any)cnvGSA_1.57.0.tar.gz(r-4.6-any)
cnvGSA_1.57.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.57.0(bioc 3.24)cnvGSA-1.56.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:b8915b8630. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 217 | ||
| linux-devel-x86_64 | NOTE | 194 | ||
| source / vignettes | OK | 181 | ||
| linux-release-x86_64 | NOTE | 239 | ||
| macos-release-arm64 | NOTE | 117 | ||
| macos-oldrel-arm64 | NOTE | 154 | ||
| windows-devel | NOTE | 507 | ||
| windows-release | NOTE | 535 | ||
| windows-oldrel | NOTE | 498 | ||
| wasm-release | OK | 134 |
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:BiocGenericsbrglmcodetoolsdata.tabledoParallelforeachgenericsGenomicRangesIRangesiteratorsprofileModelS4VectorsSeqinfosplitstackshape
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 |
