RSNPset: Efficient Score Statistics for Genome-Wide SNP Set Analysis

An implementation of the use of efficient score statistics in genome-wide SNP set analysis with complex traits. Three standard score statistics (Cox, binomial, and Gaussian) are provided, but the package is easily extensible to include others. Code implementing the inferential procedure is primarily written in C++ and utilizes parallelization of the analysis to reduce runtime. A supporting function offers simple computation of observed, permutation, and FWER and FDR adjusted p-values.

Author
Chanhee Yi, Alexander Sibley, and Kouros Owzar
Date of publication
2015-11-20 08:40:59
Maintainer
Alexander Sibley <alexander.sibley@dm.duke.edu>
License
GPL-3
Version
0.5

View on CRAN

Man pages

rsnpset
RSNPset Analysis Function
RSNPset-package
Efficient Score Statistics for Genome-Wide SNP Set Analysis
rsnpset.pvalue
RSNPset P-value Function
summary.RSNPset
RSNPset Analysis Summary Function
summary.RSNPset.pvalue
RSNPset P-value Summary Function

Files in this package

RSNPset
RSNPset/inst
RSNPset/inst/doc
RSNPset/inst/doc/RSNPset.pdf
RSNPset/inst/doc/RSNPset.R
RSNPset/inst/doc/RSNPset.Rnw
RSNPset/src
RSNPset/src/Makevars
RSNPset/src/rsnpset.cpp
RSNPset/src/Makevars.win
RSNPset/NAMESPACE
RSNPset/NEWS
RSNPset/R
RSNPset/R/summary.RSNPset.R
RSNPset/R/summary.RSNPset.pvalue.R
RSNPset/R/rsnpset.R
RSNPset/R/rsnpset.pvalue.R
RSNPset/vignettes
RSNPset/vignettes/RSNPset.Rnw
RSNPset/MD5
RSNPset/build
RSNPset/build/vignette.rds
RSNPset/DESCRIPTION
RSNPset/man
RSNPset/man/summary.RSNPset.Rd
RSNPset/man/RSNPset-package.Rd
RSNPset/man/summary.RSNPset.pvalue.Rd
RSNPset/man/rsnpset.pvalue.Rd
RSNPset/man/rsnpset.Rd