Added Xia Shen's function 'polygenic_hglm'. This procedure is functionally similar to 'polygenic', but is much faster and reports standard errors for fixed effects, which facilitates significance testing (with polygenic, the only way to test significance of a covariate was via Likelihood Ratio Test, which is rather laborious procedure).
Applied the patch of Nicola Pirastu to descriptives.trait. Bugs fixed: [#1184], [#1185], [#1259], all related to use of by.var argument: descriptives.trait can not see the variable in by.var argument unless full path specified, missings in by.var argument.
Added a number of functions facilitating relationship checks. The core function is 'findRelatives'. Compared to guessing relations from genomic kinship matrix, this procedure offers several enhancements: (1) by use of IBD/IBS 3-state space, it allows to distinguish between some pairs, which have the same kinship (e.g. parent-offspring from brother-sister; uncle-nephew from grandparent-grandchild, etc.) (2) it reports likelihood, allowing for more rigorous inferences Added one post-processing function, 'reconstructNPs', which facilitates reconstruction of nuclear pedigrees from the 'findRelatives' output.
Updated check.marker, the part related to inferences based on Y-linked markers, adding a warning if no. Y-markers is < 10
Changes in convert.snp.mach documentation to better reflect the fact that the map-file should have header; changes to convert.snp.illumina documentation to reflect the nature of the data better; added option 'mapHasHeaderLine' to convert.snp.ped and updated documentation (resolving feature request #1317).
Many thanks to Xia and Nicola, who provided extended functionality, Maria Gonic, Marcin Kierczak, LUPA workshop participants, and other people who provided important feedback and suggestions.