Description Usage Arguments Details Value Note Author(s) References See Also Examples
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.
1 | FunciSNPtable(dat, rsq, geneSum = FALSE)
|
dat |
FunciSNP data.frame: |
rsq |
an interger (0-1): |
geneSum |
logical: |
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.
Standard output which summarizes FunciSNP results.
NA
Simon G. Coetzee (maintainer: scoetzee@gmail.com); Houtan Noushmehr, PhD (houtan@usp.br)
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).
getFSNPs
, FunciSNPplot
, FunciSNPAnnotateSummary
, FunciSNPtable
, FunciSNPbed
1 2 3 4 | data(glioma);
gl <- FunciSNPAnnotateSummary(glioma);
FunciSNPtable(gl, rsq=0.5);
FunciSNPtable(gl, rsq=0.5, geneSum=TRUE);
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