Rcpp::sourceCpp('src/counts.cpp')
require(bigsnpr)
celiac <- AttachBigSNP("celiac_impute1_sub1")
#celiac <- Impute(celiac, ncores = 2, verbose = TRUE)
#celiac <- GetPhenos(celiac)
#test <- Counts(celiac)
X <- celiac$genotypes
indCase <- which(celiac$fam$pheno == 1)
indControl <- which(celiac$fam$pheno == -1)
#test <- mycount(X@address, indCase, indControl)
require(microbenchmark)
print(microbenchmark(
test <- mycount(X@address, indCase, indControl),
test2 <- mycount3(X@address, indCase, indControl),
times = 20
))
# no significant difference
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