FunciSNPAnnotateSummary {FunciSNP} | R Documentation

## Genomic Annotation of YAFSNPs.

### 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: 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

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

### Examples

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

[Package FunciSNP version 1.32.0 Index]