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Paper testing a number of different genetic distance metrics (including those used by algatr) for landscape genomics
A distance metric that can be used to test differences among individuals or populations is that of Bray-Curtis. This distance is a transformation of Jaccard’s distance (see below) and is derived from an ecological ordination paper by Bray & Curtis (1957).
11 gru 2023 · Distance weights The --distance-wts flag allows you to weight the variants in an arbitrary manner. 'exp=<x>' causes a weight of (2q(1-q))-x to be applied to each variant, where q is the loaded or inferred MAF. If a filename is provided instead, variant IDs are loaded from the first column and weights from the second.
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21 kwi 2021 · We develop gene-set distance analysis (GSDA) by generalizing distance correlations to evaluate the association of a gene set with categorical and censored event-time variables. We also develop a backward elimination procedure to identify a subset of genes that empirically drive significant associations.
24 maj 2017 · In this simulation study, we analyze the behavior of different genetic distances in Island (null hypothesis) and stepping stone models displaying varying neighborhood sizes.
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