Description Usage Arguments Value Examples
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.
1 2 3 4 5 6 7 8 | select_snps(
clumpingResult,
fdr = 0.1,
type = c("slope", "smt"),
lambda = "gaussian",
sigma = NULL,
verbose = TRUE
)
|
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 |
object of class selectionResult
1 2 3 4 | ## Not run:
slope.result <- select_snps(clumping.result, fdr=0.1)
## End(Not run)
|
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