gcat {gcatest} | R Documentation |
Performs the GCAT test for association between SNPs and trait, and returns the p-values.
gcat(X, LF, trait, adjustment = NULL) gcatest(X, LF, trait, adjustment = NULL) gcat.stat(X, LF, trait, adjustment = NULL)
X |
a matrix of SNP genotypes, i.e. an integer matrix of 0's, 1's, and 2's. Sparse matrices of class Matrix are not supported (yet). |
LF |
matrix of logistic factors outputed from function |
trait |
vector |
adjustment |
matrix of adjustment variables |
vector of p-values
gcatest
:
gcat.stat
: returns the association statistics instead of the
p-value.
Song, M, Hao, W, Storey, JD (2015). Testing for genetic associations in arbitrarily structured populations. Nat. Genet., 47, 5:550-4.
library(lfa) LF = lfa(sim_geno, 3) gcat_p = gcat(sim_geno, LF, sim_trait) gcat_stat = gcat.stat(sim_geno, LF, sim_trait)