tests/testthat/test_ld.R

In explodecomputer/simulateGP: Functions for Simulating Genotype-Phenotype Relationships

context("LD")
library(simulateGP)

test_that("get ld matrix", {

	skip("needs gwas files")
	chr <- 1
	from <- 1892607
	to <- 3582736
	bfile <- "/Users/gh13047/repo/mr-base-api/app/ld_files/EUR"
	plink_bin <- genetics.binaRies::get_plink_binary()
	a <- get_ld(chr, from, to, bfile, plink_bin)	
	expect_true(length(a) == 2)
	expect_true(nrow(a[[1]]) == nrow(a[[2]]))
	expect_true(nrow(a[[1]]) == ncol(a[[1]]))
})


test_that("test_ldobj", {
	ldobj <- test_ldobj(nsnp=1050, chunksize=100)
	expect_equal(length(ldobj), ceiling(1050/100))	
})