pvalues {jtGWAS} | R Documentation |
Method to compute the p-values for results from jtGWAS
.
pvalues(jtGWAS.object)
jtGWAS.object |
A |
A matrix of p-values with the same dimensions as the standardized statistics from jtGWAS
. If jtGWAS
was run with standardized=FALSE
, returns NULL
.
# Generate dummy data num_patient <- 100 num_marker <- 10 num_SNP <- 500 set.seed(12345) X_pat_mak <- matrix(rnorm(num_patient*num_marker), num_patient, num_marker) G_pat_SNP <- matrix(rbinom(num_patient*num_SNP, 2, 0.5), num_patient, num_SNP) colnames(X_pat_mak) <- colnames(X_pat_mak, do.NULL=FALSE, prefix="Mrk:") colnames(G_pat_SNP) <- colnames(G_pat_SNP, do.NULL=FALSE, prefix="SNP:") res <- jtGWAS(X_pat_mak, G_pat_SNP, outTopN=5) pvalues(res) res <- jtGWAS(X_pat_mak, G_pat_SNP, outTopN=NA) pvalues(res)