Version 0.32

qtl2 0.32 (2023-04-21)

Major changes

• In create_variant_query_func(), added new arguments id_field and sdp_field, and in create_gene_query_func(), added arguments name_field and strand_field (Issue #215). This gives new flexibility, but also adds new requirements (for example, that the variant database has a field "snp_id") and so could potentially break working code.

New features

• Added smooth_gmap() for smoothing out a genetic map, particularly to eliminate intervals with 0 recombination, by using a "mixture" of the map and constant recombination. Also added unsmooth_gmap() which does the reverse.

Minor changes

• read_cross2() now gives a warning if sex isn't provided but is needed. Also, if sex is missing we assume all individuals are female; previously we assumed they were male. (Issue #214)

• In plot_genes(), allow strand to be +/- 1 and not just "+" or "-". (Issue #216)

• Fixed date in citation, Broman et al. (2019) doi:10.1534/genetics.118.301595

Bug fixes

• In plot_genes() there was a case where stop was used that should have been end.