select_snps {geneSLOPE}

GWAS with SLOPE

Description

Performs GWAS with SLOPE on given snp matrix and phenotype. At first clumping procedure is performed. Highly correlated (that is stronger than parameter rho) snps are clustered. Then SLOPE is used on snp matrix which contains one representative for each clump.

Usage

select_snps(
  clumpingResult,
  fdr = 0.1,
  type = c("slope", "smt"),
  lambda = "gaussian",
  sigma = NULL,
  verbose = TRUE
)

Arguments

clumpingResult

object of class clumpingResult, clumpProcedure output.

fdr

numeric, False Discovery Rate for SLOPE.

type

method for snp selection. slope (default value) is SLOPE on clump representatives, smt is the Benjamini-Hochberg procedure on single marker test p-values for clump representatives.

lambda

lambda for SLOPE. See create_lambda.

sigma

numeric, sigma for SLOPE.

verbose

logical, if TRUE progress bar is printed.

Value

object of class selectionResult.

Examples

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)