FunciSNPtable: Will output a summary report from FunciSNP at specified...

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/funcisnp.R

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

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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

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