geneSLOPE (version 0.38.3)

select_snps: 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
)

Value

object of class selectionResult

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

Examples

if (FALSE) {
slope.result <- select_snps(clumping.result, fdr=0.1)
}