diff options
Diffstat (limited to 'issues/data/HS/fix_calc_genoprob_rqtl2_function.gmi')
| -rw-r--r-- | issues/data/HS/fix_calc_genoprob_rqtl2_function.gmi | 24 |
1 files changed, 10 insertions, 14 deletions
diff --git a/issues/data/HS/fix_calc_genoprob_rqtl2_function.gmi b/issues/data/HS/fix_calc_genoprob_rqtl2_function.gmi index a207dc76..8c4d50d2 100644 --- a/issues/data/HS/fix_calc_genoprob_rqtl2_function.gmi +++ b/issues/data/HS/fix_calc_genoprob_rqtl2_function.gmi @@ -4,7 +4,8 @@ * Assigned: Flisso * type: bug -* status: in progress +* status: in progress +* interested: alexm * key words: cross, qtl2, calc_genoprob, bugs ## Description @@ -15,7 +16,7 @@ The script is crushing as per the followin error message: calc_genoprob failing with negative length vectors are not allowed ``` For reference, see "qtl2_hmm_pipeline.R" script: -=> "https://github.com/fetche-lab/HS-rats-2026/blob/main/genotypes/new_processing/tests/chr1/codes/qtl2_hmm_pipeline.R" +=> https://github.com/fetche-lab/HS-rats-2026/blob/main/genotypes/new_processing/tests/chr1/codes/qtl2_hmm_pipeline.R The following were key findings from the run, and the error: @@ -30,16 +31,11 @@ The following were key findings from the run, and the error: * The original workflow tried to allocate a genotype-probability object effectively sized around 1499 * 50000 * 36 = 2,698,200,000, which exceeds R’s 32-bit vector-length limit (2,147,483,647), causing negative length vectors are not allowed. * So the solution was to chunk the files to 5000 lines, but still the culprit is on the calc_genoprob() runtime. -## What is already solved -* [x] error: "calc_genoprob failing with negative length vectors are not - allowed)" - -## TODO -* [] Re-run the script per specified chunks -* [] Evaluate the smoothed output for its validity and intepretability -* [] use the proximal/distal founder aware markers to extract snps from the original geno file. -* [] or, extend a function in the script to perform this -* [] Test the results with gemma and rqtl2 mapping - - +## Tasks +* [x] error: "calc_genoprob failing with negative length vectors are not allowed)" +* [ ] Re-run the script per specified chunks +* [ ] Evaluate the smoothed output for its validity and intepretability +* [ ] use the proximal/distal founder aware markers to extract snps from the original geno file. +* [ ] or, extend a function in the script to perform this +* [ ] Test the results with gemma and rqtl2 mapping |