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path: root/scripts/rqtl2_wrapper.R
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2025-04-30Revert commit dd9ef90ee89e5c075acbd5ef63cb89518e726ca3.Alexander_Kabui
2025-04-30refactor: For genetic probabilites use cores 0 to use allAlexander_Kabui
2025-04-08refactor: Explicity define no of cores for rqtl2 computation.Alexander_Kabui
2025-04-08refactor: Check for geno_tranposed and founder_geno_transposed.Alexander_Kabui
2025-03-27refactor: Temporary disable checking sex covariates in rqtl2.Alexander_Kabui
2025-03-07refactor: Construct map object from cross with columns (Marker, chr,cM, Mb).Alexander_Kabui
2025-03-07fix: Minor rqtl2 fixes.Alexander_Kabui
2025-03-07refactor rqtl2 script.Alexander_Kabui
2025-02-24Remove "generate_lod_plot" from rqtl2_wrapper.R.Munyoki Kilyungi
2025-02-21feat: Temporary disable performing genome scan with covariates for RQTL2.Alexander_Kabui
2025-02-20refactor: Skip permutation test when NO_OF_PERMUTATION less than 0.Alexander_Kabui
2025-02-20refactor: Use p=0.63 in permutation summary for suggestive threshold.Alexander_Kabui
2025-02-07fix: pass the correct genome probabilites.Alexander_Kabui
2025-02-06feat: Add the physical map file path.Alexander_Kabui
2025-02-06refactor: Rename pheno_map to physical_map .Alexander_Kabui
2025-02-06feat: Pass scan results file and genotype map file as output.Alexander_Kabui
2025-02-06feat: Modify default thresholds and write permutation results to csv file.Alexander_Kabui
2024-11-11feat: add step to insert pseudomarkers to the gmap.Alexander_Kabui
2024-11-11fix: fix issue fetching covar:Alexander_Kabui
2024-11-11refactor: rename dataset to cross.Alexander_Kabui
2024-11-11feat: add a threshold argument for lod score peak with default 1.Alexander_Kabui
2024-11-11feat: print_help when certain parameters are not provided.Alexander_Kabui
2024-11-11Refactor: remove requirement for input and output file to be in theAlexander_Kabui
2024-11-11Refactor: add better message for computation steps.Alexander_Kabui
2024-11-11refactor: refactor output for preprocessing steps.Alexander_Kabui
2024-11-11Refactor: refactor checks for working directory, input and output file.Alexander_Kabui
2024-11-11refactor: remove stringr as a script dependency:Alexander_Kabui
2024-11-11refactor: refactor for using cat and new line.Alexander_Kabui
2024-11-11refactor: use NO_OF_CORES as default and pass control file to arguments.Alexander_Kabui
2024-11-11refactor: adding pseudomarkers o genetic probabilites map.Alexander_Kabui
2024-11-11refactor: refactor printing out lod thresholds.Alexander_Kabui
2024-11-11export qtl effect plots for multi parent populations.Alexander_Kabui
2024-11-11feat: add plots for qtl effect multi parent population.Alexander_Kabui
2024-11-11feat: implementation for getting meffects for multiparent population.Alexander_Kabui
2024-11-11feat: implementation for multiparent genome scan.Alexander_Kabui
2024-11-11feat: export chromosome names and qtl effects.Alexander_Kabui
2024-11-08feat: init add functionality to estimate qtl effect.Alexander_Kabui
2024-10-30feat: add option for using pstrata for permutation.Alexander_Kabui
2024-10-30Refactor: Remove reduntant code.Alexander_Kabui
2024-10-29Refactor: pre compute kinship for both permutation and genome scan.Alexander_Kabui
2024-10-29Refactor: remove hardcoded dir_path for control files.Alexander_Kabui
2024-10-29Refactor: make plot in the temp directory passed in the script arguments.Alexander_Kabui
2024-10-29feat: add output_file as a command line argument.Alexander_Kabui
2024-10-29Refactor: ensure the temp directory is not null.Alexander_Kabui
2024-10-29feat: add optparse for the arguments.Alexander_Kabui
2024-10-29feat: write output results as json.Alexander_Kabui
2024-10-29Refactor: refactor code to find lod peaks.Alexander_Kabui
2024-10-29Refactor: refactoring for code to perform permutation tests.Alexander_Kabui
2024-10-29Refactor: refactor function to generate plots from scan1 function.Alexander_Kabui
2024-10-29Refactor: refactor method to compute scan 1.Alexander_Kabui
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