Software Open Access
choishingwan/PRSice: New Compilation and Unit Testing
Shing Wan Choi; Paul F O'Reilly; monsanto-pinheiro; wenjiany; Vinícius de Souza
Update Log
- Implement unit testing for command parsing module
- command parsing should now be more consistent and should be less likely to be source of bugs
- Now allow the use of
--a1and--a2instead of--A1and--A2to save one shift click - Can now properly handle bgen file with phasing information
- Re-implement code for covariate parsing.
--cov-factorand--cov-colshould now have a more well defined behaviour --full-backno longer require argument (the expected behaviour)- Fixed the default distance for
--clump-kb, default was Mb instead of Kb (only affects version 2.2.12) - Correctly capture negative value in
--binary-target - Correctly capture out of bound p-values and other parameters
- Use of
--memorywill no longer error out PRSice unexpectedly - Behaviour change for
--keep-ambig: Previously, when--keep-ambigwas set, PRSice will keep all ambiguous SNP and will not perform any form of flipping, e.g. strand flipping A/C to T/G or dosage flipping A/C to C/A. Now when--keep-ambigwas set, PRSice will perform dosage flipping but NOT strand flipping i.e. Base = A/T, Target = T/A, change Target dosage from 0,1,2 for T to 0,1,2 for A. You should only really use--keep-ambigif you are certain that the strand information between your base and target data are identical
Files
(197.8 MB)
| Name | Size | |
|---|---|---|
|
choishingwan/PRSice-2.2.13.zip
md5:1bb124ef3fb7696f554395458d5e65ef |
197.8 MB | Download |
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| All versions | This version | |
|---|---|---|
| Views | 716 | 603 |
| Downloads | 131 | 95 |
| Data volume | 25.9 GB | 18.8 GB |
| Unique views | 609 | 543 |
| Unique downloads | 98 | 81 |
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- Publication date:
- March 10, 2020
- DOI:
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- License (for files):
- Other (Open)