cpvSNP
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see cpvSNP.
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Bioconductor version: 3.11
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 "4.0") 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 | 1.20.0 |
In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
License | Artistic-2.0 |
Depends | R (>= 2.10), 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_1.20.0.tar.gz |
Windows Binary | cpvSNP_1.20.0.zip |
macOS 10.13 (High Sierra) | cpvSNP_1.20.0.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 |
Old Source Packages for BioC 3.11 | Source Archive |