cpvSNP
This is the released version of cpvSNP; for the devel version, see cpvSNP.
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.44.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 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_1.44.0.tar.gz |
| Windows Binary (x86_64) | cpvSNP_1.44.0.zip |
| macOS Binary (big-sur-x86_64) | cpvSNP_1.44.0.tgz |
| macOS Binary (sonoma-arm64) | cpvSNP_1.44.0.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 |