NEWS.md

In ASRgenomics: Complementary Genomic Functions

To report bugs and new features, please send a message to \emph{[e-mail]}

ASRgenomics 1.1.4 - January 25

Bug fixes:

• Minor corrections on documentation and synthetic.cross.

ASRgenomics 1.1.3 - November 25

Improvements:

• Tests have been improved.

Bug Fixes:

• Fixed RM data frame exported by match.G2A in which combinations of row and columns were being replicated.

ASRgenomics 1.1.2 - November 2nd

Improvements:

• Added a NEWS.md file to track changes to the package.

• Small internal changes for better integration with ASRgwas.

• Enabled qc.filtering to finish calculations when a single marker is left.

• Code synthetic.cross will leave only one of the records if duplicated in the pedigree.

• Code kinship.diagnostics will leave only one of the records if duplicated in the kinship matrix.

Bug Fixes:

• Now kinship.diagnostics with clean = TRUE will not crash if there is nothing to remove.

ASRgenomics 1.1.1 - July 21th

Improvements:

• Small internal changes for better integration with ASRgwas.

ASRgenomics 1.1.0 - May 25th

New Features:

• The function snp.pruning for marker pruning based has been added.

• The function synthetic.cross for obtaining the genotypes of offspring off of a set of crosses has been added.

• The function snp.recode for marker recoding has been added.

• The function H.matrix, which is a simplification of H.inverse, has been added.

• In kinship.diagnostics, an option to determine the proportion of data points to use for plotting has been added to improve processing time.

• Two new filters for markers have been added to qc.filtering, one based on inbreeding and one based on the observed heterozygosity (suggested by Simon Nadeau).

• An option to draw group-dependent ellipses has been added to both snp.pca and kinship.pca.

• Now the markers map can be passed to qc.filtering and will also be filtered.

Improvements:

• Relevant attributes of an object (such as INVERSE) are preserved after using full2sparse and sparse2full.

• Now qc.filtering can better deal with markers with all samples missing. These markers are removed first thing when the function is called.

• Plot generation in match.G2A processing time has been reduced by a factor of ~3.

• The recoding section of qc.filtering has been put into another function (snp.recode). The arguments related to recoding in the first have not been removed, but if used will generate a stop suggesting the usage of the latter. Consequently, the M.recode output has been removed.

• More message control with message = TRUE/FALSE has been added to several functions.

• Some internal linear algebra has been changed to improve processing time.

• Error handling has been improved in G.inverse to provide more informative messages to the user.

• Help files have been reviewed and improved.

Bug Fixes:

• Now the colNames attribute is correctly assigned in full2sparse.

ASRgenomics documentation built on May 29, 2024, 12:03 p.m.