cpvSNP
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Bioconductor version: Release (3.20)
Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.
Author: Caitlin McHugh, Jessica Larson, and Jason Hackney
Maintainer: Caitlin McHugh <mchughc at uw.edu>
citation("cpvSNP")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cpvSNP")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cpvSNP")| Running gene set analyses with the "cpvSNP" package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneSetEnrichment, Genetics, GenomicVariation, Pathways, Software, StatisticalMethod |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), GenomicFeatures, GSEABase(>= 1.24.0) |
| Imports | methods, corpcor, BiocParallel, ggplot2, plyr |
| System Requirements | |
| URL |
See More
| Suggests | TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cpvSNP_1.38.0.tar.gz |
| Windows Binary (x86_64) | cpvSNP_1.38.0.zip |
| macOS Binary (x86_64) | cpvSNP_1.38.0.tgz |
| macOS Binary (arm64) | cpvSNP_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cpvSNP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cpvSNP |
| Bioc Package Browser | https://code.bioconductor.org/browse/cpvSNP/ |
| Package Short Url | https://bioconductor.org/packages/cpvSNP/ |
| Package Downloads Report | Download Stats |