select_snps: GWAS with SLOPE

In psobczyk/geneSLOPE: Genome-Wide Association Study with SLOPE

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	clumpProcedure output
fdr	numeric, False Discovery Rate for SLOPE
type	method for snp selection. slope (default value) is SLOPE on clump representatives, smt is 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

## Not run: 
slope.result <- select_snps(clumping.result, fdr=0.1)

## End(Not run)

psobczyk/geneSLOPE documentation built on July 5, 2025, 1:23 a.m.