GWAS calculation #4
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During MapMutations we have all the information we need to track
how many individuals are coalescing (for diploids) at each node
that is visited/created. We pay essentially no cost for computing
this, and its about 1% increase in GRG size.
This is now accessible from grgl::NodeData via the
numIndividualCoals field, and is extremely useful for any
computations that requires {0, 1, 2} form for the matrix version
of the computation.
Added the copying of NodeData in GRG merge operation, since we
now have more than populationId (it should have always been copied)
* Add "zygosity information" command: Similar to allele frequency, but emits the individual-based stats of how many AA, Aa, aa that are for each variant. * Better way to emit sorted calculations on mutations. New API method getMutationsToNodeOrdered() emits nodes and mutation IDs ordered by mutation position and allele. * If you don't specify a phenotype file it will now use a random vector. * New flag --beta-only only calculates beta (the dot product), not the additional statistics surrounding it (like plink does). * GWAS can compute just beta (to mimic the dot-product calculation of XSI, which we compare against) or all of the fields necessary. * Zygosity info breaks down how many individuals are hetero or homozygous in a particular variant. * We optionally link in GNU Scientific Library (GSL) for computing p-values for GWAS. Use -DENABLE_GSL=ON to enable this, other the p-value will just be NaN (with a warning).
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Perform GWAS using GRG.