| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |
| GeneNetwork3 REST API for data science and machine learning |
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