FunciSNPAnnotateSummary: Genomic Annotation of YAFSNPs.

In FunciSNP: Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

Description

This will annotate all identified YAFSNP for it's distance to the nearest known TSS, whether it overlapps a known exon, intron, 5'UTR, 3'UTR, promoter, lincRNA or in gene desert (intergentic) regions.

Usage

FunciSNPAnnotateSummary(snp.list)

Arguments

snp.list

a FunciSNP object: snp.list represents the FunciSNP object output from FunciSNP. See getFSNPs.

Details

All known genomic features (exon, intron, 5'UTR, 3'UTR, promoter, lincRNA or in gene desert (intergentic)) are used to annotate the newly identified YAFSNP. Information described in this data.frame is used for all summary plots, table, and bed file generations.

Value

data.frame with rows for each correlated SNP.

Note

NA

Author(s)

Simon G. Coetzee (maintainer: [e-mail]); Houtan Noushmehr, PhD ([e-mail])

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

getFSNPs, FunciSNPplot, FunciSNPAnnotateSummary, FunciSNPtable, FunciSNPbed

Examples

data(glioma);
gl <- FunciSNPAnnotateSummary(glioma);
dim(gl)
head(gl)
names(gl)

FunciSNP documentation built on Nov. 8, 2020, 4:56 p.m.