select_snps {geneSLOPE} | R Documentation |
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 |
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)
[Package geneSLOPE version 0.38.3 Index]