tests/testthat/test_manipulate.r

In MRCIEU/gwasvcf: Tools for Dealing with GWAS Summary Data in VCF Format

context("VCF manipulations")
library(gwasvcf)
library(magrittr)
library(dplyr)

fn <- system.file("extdata","data.vcf.gz", package="gwasvcf")
vcf1 <- VariantAnnotation::readVcf(fn)[1:70,]
vcf2 <- VariantAnnotation::readVcf(fn)[40:90,]
vcf3 <- VariantAnnotation::readVcf(fn)[60:92,]
vcf4 <- VariantAnnotation::readVcf(fn)[65:92,]
l <- list(vcf1, vcf2, vcf3, vcf4)
if (Sys.info()["sysname"] != "Windows") set_bcftools()

# Need to check what happens with multiallelic variants

test_that("vcflist_overlaps", {
  skip_on_os("windows")
  
	o <- vcflist_overlaps(vcflist=list(vcf1, vcf2), chrompos=NULL)
	expect_true(all(sapply(o, length) == 31) & length(o) == 2)

	o <- vcflist_overlaps(vcflist=list(vcf1, vcf2, vcf3, fn), chrompos="1:1-10000000")
	expect_true(all(sapply(o, length) == 11) & length(o) == 4)

	o <- vcflist_overlaps(vcflist=list(vcf1, vcf2, vcf3, vcf4), chrompos="1:1-10000000")
	expect_true(all(sapply(o, length) == 6) & length(o) == 4)

	o <- vcflist_overlaps(vcflist=list(fn, fn), chrompos="1:1-10000000")
	expect_true(all(sapply(o, length) == 92) & length(o) == 2)

	o <- vcflist_overlaps(vcflist=list(fn, fn), chrompos="2:1-10000000")
	expect_true(all(sapply(o, length) == 0) & length(o) == 2)	
})


fn <- system.file("extdata","data.vcf.gz", package="gwasvcf")
V <- VariantAnnotation::readVcf(fn) 
vv <- V %>% vcf_to_granges %>% dplyr::as_tibble()

test_that("create vcf", {
	out <- vv %$% create_vcf(chrom=seqnames, pos=start, nea=REF, ea=ALT, snp=ID, ea_af=AF, effect=ES, se=SE, pval=10^-LP, n=SS, name="a")
	VariantAnnotation::writeVcf(out, file="temp.vcf")
	expect_true(file.exists("temp.vcf"))
})