gcat | R Documentation |
Performs the GCAT association test between SNPs and trait, returning 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, 2's and |
LF |
matrix of logistic factors from |
trait |
vector |
adjustment |
matrix of adjustment variables |
vector of p-values
gcatest()
: Alias of gcat
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)
# make example data smaller so example is fast
# goes from 1000 to 100 individuals
indexes <- sample.int( ncol(sim_geno), 100 )
sim_geno <- sim_geno[ , indexes ]
sim_trait <- sim_trait[ indexes ]
# now run LFA and GCATest
LF <- lfa(sim_geno, 3)
gcat_p <- gcat(sim_geno, LF, sim_trait)
gcat_stat <- gcat.stat(sim_geno, LF, sim_trait)
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