geneSLOPE: Genome-Wide Association Study with SLOPE

Description Details Author(s) References Examples

Description

Package geneSLOPE performes genome-wide association study (GWAS) with SLOPE, short for Sorted L-One Penalized Estimation. SLOPE is a method for estimating the vector of coefficients in linear model. For details about it see references.

Details

GWAS is splitted into three steps.

Version: 0.37.0

Author(s)

Malgorzata Bogdan, Damian Brzyski, Emmanuel J. Candes, Christine Peterson, Chiara Sabatti, Piotr Sobczyk

Maintainer: Piotr Sobczyk [email protected]

References

SLOPE – Adaptive Variable Selection via Convex Optimization, Malgorzata Bogdan, Ewout van den Berg, Chiara Sabatti, Weijie Su and Emmanuel Candes

Examples

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famFile <- system.file("extdata", "plinkPhenotypeExample.fam", package = "geneSLOPE")
mapFile <- system.file("extdata", "plinkMapExample.map", package = "geneSLOPE")
snpsFile <- system.file("extdata", "plinkDataExample.raw", package = "geneSLOPE")
phe <- read_phenotype(filename = famFile)
screening.result <- screen_snps(snpsFile, mapFile, phe, pValMax = 0.05, chunkSize = 1e2)
clumping.result <- clump_snps(screening.result, rho = 0.3, verbose = TRUE)
slope.result <- select_snps(clumping.result, fdr=0.1)

## Not run: 
gui_geneSLOPE()

## End(Not run)

geneSLOPE documentation built on May 30, 2017, 1:22 a.m.