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.


News

RSNPset v0.5.3 (Release date: 2017-12-11)

  • Minor bug fix for example code in function documentation

RSNPset v0.5.2 (Release date: 2017-02-20)

  • Minor bug fix for note about registering native routines under r-devel

RSNPset v0.5.1 (Release date: 2017-02-16)

  • Minor bug fix for warnings in vingette under r-devel
  • Changed names of two returned columns in rsnpset.pvalue() (and associated documentation) for consistency

RSNPset v0.5 (Release date: 2015-11-05)

  • Authors now recommend pruning SNPs when using the Cox score statistic (method=”cox”)
  • Documentation updates and corrections

RSNPset v0.4 (Release date: 2015-02-11)

  • Addition of NEWS file
  • Implementation of argument X (covariates) in rsnpset() for score="gaussian"
  • New option/default for rsnpset() argument r.method="monte carlo"
  • New default for rsnpset() argument v.permute="FALSE"
  • New attribute for RSNPset S3 objects: "r.method", now expected by summary.RSNPset()
  • Elements of results list for RSNPset S3 objects renamed to "Observed", "Replication.1", "Replication.2", ...
  • Argument pval.transform=TRUE now allowed in rspset.pvalue() for rsnpset() results with return.rank=FALSE

RSNPset v0.3 (Release date: 2014-12-16)

  • Change of Maintainer

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("RSNPset")

0.5.3 by Alexander Sibley, a year ago


Browse source code at https://github.com/cran/RSNPset


Authors: Chanhee Yi , Alexander Sibley , and Kouros Owzar


Documentation:   PDF Manual  


GPL-3 license


Imports fastmatch, foreach, doRNG, qvalue, Rcpp

Suggests knitr

Linking to Rcpp, RcppEigen


See at CRAN