FunciSNP (version 1.14.0)

FunciSNPtable: 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.

Value

Standard output which summarizes FunciSNP results.

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.

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);