filter_taxa_from_input: Filter taxa from a loaded dataset

In leffj/mctoolsr: Microbial Community Data Analysis Tools

Filter taxa from a loaded dataset

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. Taxa are found using grep, so it is not necessary to use the entire names of taxa as long as they are not ambiguous. Can filter using taxa IDs (i.e. row names in taxa table).

Usage

filter_taxa_from_input(
  input,
  filter_thresh,
  taxa_to_keep,
  taxa_to_remove,
  at_spec_level,
  taxa_IDs_to_keep,
  taxa_IDs_to_remove
)

Arguments

input	Input data (a list variable) from load_taxa_table().
filter_thresh	Filter OTUs less than this number based on mean OTU 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.
at_spec_level	If included, only keep/remove matches at this specific taxonomy level(s) (a number/numbers referring to the taxonomy column(s)).
taxa_IDs_to_keep	Keep only taxa with these IDs (row names).
taxa_IDs_to_remove	Remove taxa with these IDs (row names).

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