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Created with Raphaël 2.2.08Feb517Nov2Oct14Jul30Jun13Jan1Apr29Mar11Jan1Oct13Aug76Mar30Nov30Oct20627Sep11Aug325Jul13Jun226May23161124Apr211023Mar27Feb2115Added the PolyHaplotyper_small dataset and a minot correctionmastermasterAdded examples and other fixes to meet CRAN requirementsLast changes (hopefully) for publication: demo data for vignette changed, removed the "options" way to specify the ahcdir and to load the ahc(complete)lists, other minor internal changesAnonymized demo data; fixed import of XML package; lots of code and documentation cleanups; adapted vignette to some changed function callsRevert "Major revision 20200713: (1) more parental combinations are considered to fit FS families, (2) imputation within FS families added, (3) general code cleanup"Major revision 20200713: (1) more parental combinations are considered to fit FS families, (2) imputation within FS families added, (3) general code cleanupminor changes in DESCRIPTION, testthat, vignette until 20200114Several bugs fixed as reported by Peter and Giorgio nov-dec 2019Corrected the vignette and some roxygen documentationBug fixes and some documentation improvementsCompletely revised. New loop structure to iterate until set of solutions over all F1 groups doesn't change anymore. Also use the column number in the ahc(complete)list item for the mrkdid to indicate the hapcomb: one nr instead of ploidy or 2^nmrk numbers. Perform check for parents of non-fitted F1s and delete hapcomb if conflicting with progeny.Some corrected comments and documentation; a correction in loadAllHaploCombList. New function getNewMrkdids to pre-calculate all mrkdids in case completeahclist is available.Corrected and updated help texts, vignette, a.o. toLarge code and comments cleanup; duplicated part of hapOneBlock as function; pedigreeHapdosCheck renamed to pedigreeHapCheck (and many more variables and functions renamed to reflect change from hapdos to hapcomb); showOneF1 works againVersion 0.2.1 Major changes, a.o. storing ahc(complete)lists as hap combinations instead of hap dosages (much smaller); treating F1s with shared parents as one group. Minor bugfix vs workshop version; expanding parental combination search if no acceptable P-values found; allhap is not an element of the inferHaplotypes result anymore (replaced by functions allhap and usedhap)Solved bug in processSOFbug in calcStatistics when only one haploblock; solvedSome bug fixes for haploblocks with only 1 markerin single_cycle_infer: changed the selection criterion for haploype combinationsSome bug fixes; streamlined hapOneBlockinferHaplotypes uses new criterion to select haplotype combinations (least nr of new haplotypes, not only highest dosage of known haplotypes)Large cleanup and revision of code, documentation and vignette. Main function renamed from solveAllHaploblocks to inferHaplotypes.Improved function solveOneF1, cleaned up the code, extended vignetteVignette and data added, some functions renamedvarious bug fixes, new function haploblock_df2listAdded several diagnostics, overview and summary functions and some extra documentationAdded and tested pedigreeHapdosCheck and expandHapdosImprovements debugged. Results more trustworthy (though less appealing) than pervious working version.rewrote haplotypeDosagesF1 to use segregation rates (untested yet). Found that "%" in roxygen docs is deadly!Bug fixes; more output in haplotypeDosagesF1; works through Geert's 4- and 5-SNP data of March 2017Lots of bug fixes. Geert's original dat now run fine again.new function solveAllHaploblocks. Still checking first 4 of Geerts "old" haploblocks with haplotypeDosagesF1 (much slower!)new untested haplotypeDosagesF1 for multiple F1s. Issues with ahc(complete)list in check packagenew completeAllHaploComb. Start with use of multiple F1 populations.many changes, esp. in allHaploComb and haplotypeDosagesF1; global variables ahcploidy and ahclistsecond minfrac valueimprovement of haplotypeDosagesF1. Replaced all (contig) alleles by haplotypes.First commit; working version with documentation.