FunciSNP-package {FunciSNP} | R Documentation

## Functional Identification of SNPs with Phenotype by Coincidence with Chromatin Biofeatures

### Description

The package includes functions to identify and annotate putative functional SNPs using information derived from GWAS, 1000 genomes database, and sequences around peaks.

### Details

Package: | FunciSNP
Type: | Package
Version: | 0.99.0
Date: | 2012-05-18
License: | GPL-3
LazyLoad: | yes

### Author(s)

Simon G. Coetzee (maintainer: scoetzee@gmail.com); Houtan Noushmehr, PhD (houtan@usp.br)

### References

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).

### See Also

`FunciSNPplot`, `FunciSNPAnnotateSummary`, `FunciSNPtable`, `FunciSNPbed`

### Examples

    ##
    ## 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);

[Package FunciSNP version 1.28.0 Index]