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Diffstat (limited to 'e2e-tests/hsmice/jwas-manhattan.r')
| -rw-r--r-- | e2e-tests/hsmice/jwas-manhattan.r | 13 |
1 files changed, 13 insertions, 0 deletions
diff --git a/e2e-tests/hsmice/jwas-manhattan.r b/e2e-tests/hsmice/jwas-manhattan.r new file mode 100644 index 0000000..a437a8c --- /dev/null +++ b/e2e-tests/hsmice/jwas-manhattan.r @@ -0,0 +1,13 @@ +library(dplyr) +library(qqman) +library(readr) + +args = commandArgs(trailingOnly=TRUE) +if (length(args) != 1) { + write("Usage: Rscript jwas-manhattan.r GWAS-FILE", stderr()) + quit(status=1) +} +gwas_file = args[1] + +gwas = mutate(read_tsv(gwas_file), antilog=10^(-modelfrequency)) +manhattan(gwas, chr="chromosome", bp="position", snp="marker_ID", p="antilog") |