filter_taxa_from_table: Filter taxa from an individual taxa summary table

In leffj/mctoolsr: Microbial Community Data Analysis Tools

Filter taxa from an individual taxa summary table

Description

Can use one or more of the parameters to do filtering. Threshold filtering takes precidence over taxa filtering. If taxa to keep and taxa to remove are both included, taxa to remove will be removed if the parameter entries conflict. Note that taxa string matching uses grep, so you can provide partial taxa strings. However, if there are multiple matches, all matching taxa will be removed.

Usage

filter_taxa_from_table(tax_table, filter_thresh, taxa_to_keep, taxa_to_remove)

Arguments

tax_table	Input taxa summary table from summarize_taxonomy (dataframe).
filter_thresh	Filter taxa less than this number based on mean table values.
taxa_to_keep	Keep only taxa that contain these names. Vector or string.
taxa_to_remove	Remove taxa that contain these names. Vector or string.

leffj/mctoolsr documentation built on Aug. 5, 2022, 1:27 a.m.