stratify: Get the phylostratum of each query gene

In arendsee/phylostratr: Analyze phylostratigraphic data

Get the phylostratum of each query gene

Description

Get the phylostratum of each query gene

Usage

stratify(
  hittable,
  classifier = classify_by_adjusted_pvalue(0.001),
  strata_names = get_mrca_names(hittable)
)

Arguments

hittable	data.frame with the columns 'qseqid', 'mrca', 'ps', and whichever columns arerequired by 'classifier'
classifier	A function to infer homology between the query gene and a specific subject
strata_names	A factor of MRCA names (scientific names by default, but you can set your own labels) with levels ordered by phylostrata. This must be a named factor, with names corresponding to taxon IDs. It is used to make the mrca_name column. It will be used mostly in plots and reports; internally the taxon ids are used.

arendsee/phylostratr documentation built on Dec. 23, 2024, 1:31 p.m.