- Solved a phenotype naming bug. The original phenotype names were not kept in the output of map.QTL.
- In the function map.QTL the argument k has been renamed knn, to avoid confusion with the K argument used for kinship.
- sample.cM has been renamed sample.markers and the cM parameter renamed binsize.
- plot.LD renamed plot_LD.
- The output residuals table was fixed. It had an incorrect order for phenotypes containing missing values.
- Fix a small bug in plot_LD causing an error when using less than four quantiles.
- Error in sample.cM when using a vector of marker names as input.
- Error in QQ.plot using a list of p-values as input.
- Fix bugs in pheno_box, that was returning errors when NAs were in SNP dosages or haplotypes or phenotypes.
- Fix a bug introduced in a late version of impute.knn.
- Changes in roxygen tags.
- Include examples.
- Resize the example dataset (in data/) to fit in 1 Mb.
- Add documentation for datasets.
Version distributed to partners at the software workshop in December 2020.
- Better implementation for continuous genotypes. Changes in functions for input checking and impute.knn to allow continuous genotypes.
- More formal input checks. Regarding this, the function orderInput has been added, that orders all the input matrices. To be used before running map.QTL.
- skyplot function. A few new arguments in the function skyplot for more flexibility (e.g. adjust distance between chromosomes, use user-defined colors). Also, plotting time has been considerably reduced.
- In the skyplot function, a bug related to marker order has been fixed.
- Multiple cofactors passed to the argument cofactor of map.QTL were not read correctly (only the first one was actually read).
Version released for the software workshop in December 2019.