/usr/lib/R/site-library/VariantAnnotation/unitTests/test_snpSummary.R is in r-bioc-variantannotation 1.20.2-1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | test_snpSummary_empty <- function()
{
cnames <- c("g00", "g01", "g11", "a0Freq", "a1Freq",
"HWEzscore", "HWEpvalue")
## no genotype
fl <- system.file("unitTests", "cases",
"FORMAT_header_no_SAMPLEs.vcf",
package="VariantAnnotation")
res <- suppressWarnings(snpSummary(readVcf(fl, "hg19")))
checkTrue(all(dim(res) == c(0L, 7L)))
checkEquals(names(res), cnames)
## structural
fl <- system.file("extdata", "structural.vcf",
package="VariantAnnotation")
res <- suppressWarnings(snpSummary(readVcf(fl, "hg19")))
checkTrue(all(dim(res) == c(0L, 7L)))
checkEquals(names(res), cnames)
}
test_snpSummary_output <- function()
{
fl <- system.file("extdata", "ex2.vcf",
package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
res <- snpSummary(vcf)
checkTrue(is.integer(res$g00))
checkTrue(is.integer(res$g01))
checkTrue(is.integer(res$g11))
checkEquals(nrow(res), nrow(vcf))
checkEquals(rownames(res), rownames(vcf))
checkEquals(as.integer(res[1,c("g00", "g01", "g11")]), c(1L, 1L, 1L))
checkEquals(as.integer(res[2,c("g00", "g01", "g11")]), c(2L, 1L, 0L))
checkEquals(round(res[["a0Freq"]], 2), c(0.50, 0.83, NA, NA, NA))
checkEquals(round(res[["a1Freq"]], 2), c(0.50, 0.17, NA, NA, NA))
}
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