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| author | Arun Isaac | 2025-11-13 02:23:34 +0000 |
|---|---|---|
| committer | Arun Isaac | 2025-11-13 02:23:34 +0000 |
| commit | 2bd7b74814ca208a30382c6ad847e169addc542d (patch) | |
| tree | 89d51b7a3aeffe759474e52ae104ed9f1b74646e /e2e-tests/hsmice/jwas-manhattan.r | |
| parent | f0076f0a413ad3706e3b012b07e4a14c61c79b6e (diff) | |
| download | pyhegp-2bd7b74814ca208a30382c6ad847e169addc542d.tar.gz pyhegp-2bd7b74814ca208a30382c6ad847e169addc542d.tar.lz pyhegp-2bd7b74814ca208a30382c6ad847e169addc542d.zip | |
Add JWAS tests to HSmice test.
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") |