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NEWS
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Changes in 0.46
* improved VCF parsing of model params for gbs(model.file=FALSE)
Changes in 0.45
* G_mat has option for allele matching (AM) coefficient
* Updated CDF1 analysis in madc
Changes in 0.44
* G_mat has option for reference allele frequency
Changes in 0.43
* impute_L2H was missing mean/mode imputation for CSV input
* changed default n.mark to 100 for impute_L2H
Changes in 0.42
* new option "model.fit" in gbs function
* check_ploidy accepts VCF input
Changes in 0.41
* Generalized data input for madc
Changes in 0.40
* OFP20 option in madc
Changes in 0.39
* Changed impute_PO to impute_LA to allow for other methods eventually (MAPpoly)
Changes in 0.38
* Added chunk.size option to gbs
* exception handling in impute_L2H
Changes in 0.37
* Vignette 3
Changes in 0.36
* PolyOrigin option moved to impute_PO
* GT2DS has multicore option
* internal changes for impute_L2H
Changes in 0.34
* GT2DS function has diploidize option
* impute_L2H has PolyOrigin ("PO") option
* madc function
* vcf2csv function
Changes in 0.33
* updates to gbs function
* fr2vcf renamed to array2vcf, now with options for both long and wide format
* created impute_L2H function
* update_alias removes leading zeros in progeny id
Changes in 0.32
* handling of missing AD in gbs
Changes in 0.31
* fr2vcf function
Changes in 0.30
* minor bug in impute
Changes in 0.29
* modified dart_tag to become dart2vcf
* new functions gbs, impute, write_vcf
Changes in 0.28
* new function array2VCF for storing SNP array data in VCF
Changes in 0.27
* dart_tag function has option to output B allele dosage
* update_alias can be used to update file
Changes in 0.26
* Added dart_tag function
* updated potato_V3array_map.csv with REF column for dart_tag
* fixed readXY bug due to changes in tidyr
* fixed slight bug in merge_impute
Changes in 0.25
* Moved functions for stage-wise analysis to R package StageWise
Changes in 0.24
* Fixed naming conflict in Stage2
Changes in 0.23
* Changes to multi-trait functionality
Changes in 0.22
* Completed multi-trait functionality for Stage2 and predict_MME
Changes in 0.21
* Changed name of argument in predict_MME to mask
* Conditioning of kernel matrices in Stage2
Changes in 0.20
* Changes in Stage2
Changes in 0.19
* Added cross-validation to Vignette 3 and predict_MME
Changes in 0.18
* Completed Vignette 3 for genomic selection.
* Modifications to Stage1, Stage2_prep, Stage2
* Added function dart_tag
Changes in 0.17
* Updated sparse matrix handling for stage wise analysis
Changes in 0.16
* Added PSD to Omega in Stage2
Changes in 0.15
* Major revisions to functions for two-stage analysis
Changes in 0.14
* Major revisions to functions for two-stage analysis
Changes in 0.13
* Removed some poor markers from V3array_model
* Fixed error with trim_ped
Changes in 0.12
* Changed G_coeff to G_mat
* Added several new functions for genomic selection
Changes in 0.11
* Options for axis limits in GvsA