FunciSNP-package {FunciSNP} | R Documentation |
The package includes functions to identify and annotate putative functional SNPs using information derived from GWAS, 1000 genomes database, and sequences around peaks.
Package: | FunciSNP |
Type: | Package |
Version: | 0.99.0 |
Date: | 2012-05-18 |
License: | GPL-3 |
LazyLoad: | yes |
Simon G. Coetzee (maintainer: scoetzee@gmail.com); Houtan Noushmehr, PhD (houtan@usp.br)
SG. Coetzee, SK. Rhie, BP. Berman, GA. Coetzee and H. Noushmehr, FunciSNP: An R/Bioconductor Tool Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs., Nucleic Acids Research, In press, 2012 (doi:10.1093/nar/gks542).
FunciSNPplot
, FunciSNPAnnotateSummary
, FunciSNPtable
, FunciSNPbed
## ## Glioblastoma analysis using FunciSNP ## ## Full path to the example regions file for Glioblastoma # (collected from SNPedia) glioma.snp <- file.path(system.file('extdata', package='FunciSNP'), dir(system.file('extdata',package='FunciSNP'), pattern='.snp$')); ## Full path to the example biological features BED files # derived from the ENCODE project for Glioblastoma U-87 # cell lines. glioma.bio <- system.file('extdata',package='FunciSNP'); ## FunciSNP analysis, extracts correlated SNPs from the # 1000 genomes db ("ncbi") and finds overlaps between # correlated SNP and biological features and then # calculates LD (Rsquare, Dprime, distance, p-value). # Do not run. Can take more than 5 min depending on internet connection and number of CPUs. #glioma <- FunciSNP(snp.regions.file=glioma.snp, # bio.features.loc = glioma.bio, bio.features.TSS=FALSE); ## data(glioma); class(glioma); glioma; summary(glioma);