tmp-tests/test-univRegLinCovar2.R

In privefl/bigstatsr: Statistical Tools for Filebacked Big Matrices

require(bigsnpr)
require(bigstatsr)

celiac <- AttachBigSNP("../bigsnpr/backingfiles/celiac_impute1_sub1.bk")
X <- celiac$genotypes
n <- nrow(X)
K <- 10
covar <- matrix(0, n, K)
covar[] <- rnorm(length(covar))

print(system.time(
  test <- big_univRegLin(X, rnorm(n), covar.train = covar)
))

str(test)
man <- data.frame(CHR = celiac$map$chromosome,
                  BP = celiac$map$physical.pos,
                  P = test$p.value,
                  SNP = celiac$map$marker.ID)

require(manhattanly)
manhattanly(man, snp = "SNP")
qqly(man, snp = "SNP")