FunciSNPtable {FunciSNP} | R Documentation

## Will output a summary report from FunciSNP at specified Rsquare cut-offs.

### Description

Using a specified Rsquare value (0-1) to subset the data, a table is generated which summarizes the total number of YAFSNPs, associated tagSNPs, and number of overlapping biofeatures.

### Usage

    FunciSNPtable(dat, rsq, geneSum = FALSE)

### Arguments

`dat` | FunciSNP data.frame: `dat` is a data.frame object from FunciSNPAnnotateSummary. Need to run `FunciSNPAnnotateSummary` first.
`rsq` | an interger (0-1): `rsq` is the Rsquared cutoff used to subset.
`geneSum` | logical: `geneSum` is set to FALSE. Setting to TRUE will output a list of Gene names which are nearest to the YAFSNP.

### Details

Using a specified Rsquare value (0-1) to subset the data, a table is generated which summarizes the total number of YAFSNPs, associated tagSNPs, and number of overlapping biofeatures. This will provide user a first look at the total number of available YAFSNP at a particular Rsquare cutoff. If geneSum is set to TRUE, a list of gene names is reported instead.

### Value

Standard output which summarizes FunciSNP results.

### 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);
    FunciSNPtable(gl, rsq=0.5);
    FunciSNPtable(gl, rsq=0.5, geneSum=TRUE);

[Package FunciSNP version 1.28.0 Index]