filter_feature_table: Filter phyloseq object based on samples and taxa.

In antonioggsousa/micrUBIfuns: Set of functions for microbiome analyses

Description

Filter phyloseq object based on samples and taxa names or minimum number of reads.

Usage

filter_feature_table(
  physeq,
  taxa2filter = NULL,
  samples2filter = NULL,
  min_sample_depth = 0,
  min_taxa_counts = 0
)

Arguments

physeq	phyloseq-class object.
taxa2filter	taxonomic names to exclude (character). It can include the taxa names, i.e., OTU/ASV ids - 'taxa_names(physeq)'. Also it can be instead a logical of the same length as OTU/ASV ids (i.e., 'length(taxa_names(physeq))'), where 'TRUE' represents the taxa to keep and 'FALSE' to remove. Default 'NULL'.
samples2filter	name of the samples to discard (character). Default 'NULL'.
min_sample_depth	minimum number of reads per sample to keep a sample (numeric). Default '0'.
min_taxa_counts	minimum number of reads per feature i.e., OTU/ASV, to keep a feature (features sum across samples) (numeric). Default '0'.

Value

A phyloseq object filtered.

antonioggsousa/micrUBIfuns documentation built on Nov. 14, 2020, 1:40 a.m.