| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-09-27 | Fix R/qtl output paths | zsloan | |
| The script now takes the --outdir parameter as the output directory, only using TMPDIR if nothing is passed "output" in the output directory was also changed to "gn3" to be consistent with recent changes to GN3's code | |||
| 2024-09-12 | Make sure dir exists before running R/qtl | Pjotr Prins | |
| 2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins | |
| 2024-07-08 | Pass output directory to R/qtl script instead of pulling it from the | zsloan | |
| environment Also fixes issue where the control marker keyword was wrong | |||
| 2022-03-22 | Merge branch 'feature/add_rqtl_pairscan' of ↵ | zsloan | |
| https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan | |||
| 2022-03-22 | Change order of if statements for running genoprob command | zsloan | |
| Now it checks for pairscan first, just in case interval ends up being passed (which is an irrelevant parameter for pairscan) Also added a couple more verbose prints | |||
| 2022-03-22 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ↵ | zsloan | |
| we need the list of markers/pseudomarkers and their positions) | |||
| 2022-03-22 | Added line priting pair-scan results to CSV and changed the default ↵ | zsloan | |
| step-size to 10cM for pair-scan | |||
| 2022-03-22 | - Added scan_func function that determines whether scanone or scantwo | zsloan | |
| (pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints | |||
| 2022-03-22 | Added option for running pairscan to rqtl_wrapper.R | zsloan | |
| 2022-02-02 | Fix R/qtl covar bug | zsloan | |
| The rqtl_wrapper script was throwing an error when only a single categorical covariate was used. This is apparently because "covars[,name]" throws an error in such a situation. Using just "covars" in such a situation prevents the error. So I just added an if statement checking the number of covariates. There might be some better way to deal with this in R, but this is the best I could come up with. | |||
| 2021-11-11 | Merge branch 'main' into feature/add_rqtl_pairscan | zsloan | |
| 2021-10-14 | Fixed when model is set to account for situations with no covariates | zsloan | |
| 2021-10-14 | Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.R | zsloan | |
| 2021-09-23 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ↵ | zsloan | |
| we need the list of markers/pseudomarkers and their positions) | |||
| 2021-09-23 | Added line priting pair-scan results to CSV and changed the default ↵ | zsloan | |
| step-size to 10cM for pair-scan | |||
| 2021-09-23 | - Added scan_func function that determines whether scanone or scantwo | zsloan | |
| (pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints | |||
| 2021-09-23 | Added option for running pairscan to rqtl_wrapper.R | zsloan | |
| 2021-09-23 | Fix covariates as described by Danny | zsloan | |
| 2021-08-28 | Fix issue that caused R/qtl to not use the first covariate when using ↵ | zsloan | |
| stratified permutations + covariates | |||
| 2021-08-26 | Added # permutations to verbose print | zsloan | |
| 2021-06-18 | Added option for enabling permutation strata | zsloan | |
| Fixed issue where covariates with numerical names were being ignored Fixed issue where the hash filename wasn't being used for the permutation output | |||
| 2021-06-18 | Add rqtl_wrapper.R script and necessary imports to guix.scm | zsloan | |
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index : genenetwork3 | |
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