Make biomart query permissive to more organisms #168
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Fixes #167 and #138. Proposes changes to functions
get_biomart
andplot_sexcheck_pca
Changes to
get_biomart
:grep
to search for columns with "symbol".Changes to
plot_sexcheck_pca
:get_biomart
with the counts gene features therefore the gene list in the biomart query object will match counts. Since the function looks for whether these markers correlates to PCs, the presence of the markers (and the matching ensembl gene id) are required. This function independently might benefit from an error, but since this is a non-essential step of the workflow, we want to return a message.chromosome_name
remains hard coded. Not sure if that will present a future problem.