Closed bschilder closed 3 years ago
Note sure what's wrong with this:
test_that("Filter SNPs where INFO<0.9", {
file <- tempfile()
#write the Educational Attainment GWAS to a temp file for testing
eduAttainOkbay <- readLines(system.file("extdata","eduAttainOkbay.txt",
package="MungeSumstats"))
writeLines(eduAttainOkbay,con = file)
#read it in and make N
sumstats_dt <- data.table::fread(file, nThread = 1)
#Add N column and make it not an integer
set.seed(101)
sumstats_dt[,INFO:=runif(nrow(sumstats_dt))*2]
#get SNPs with INFO<0.9
rmv_snps <- sumstats_dt[INFO<0.9,]$MarkerName
data.table::fwrite(x=sumstats_dt, file=file, sep="\t")
#Run MungeSumstats code
reformatted <- MungeSumstats::format_sumstats(file,ref_genome="GRCh37",
INFO_filter = 0.9,
on_ref_genome = FALSE,
strand_ambig_filter=FALSE,
bi_allelic_filter=FALSE,
allele_flip_check=FALSE)
res_dt <- data.table::fread(reformatted, nThread = 1)
testthat::expect_equal(all(!rmv_snps %in% res_dt$SNP),TRUE)
})
I think these were just missing an extra empty line after the function 🤷
Fixed.