filter_taxa: Filter taxa based on across-sample OTU abundance criteria

In mikemc/tidyseq: Phyloseq extensions and improvements

Description

Wrappers around phyloseq::filter_taxa that allow using a purrr-style anonymous function for .f.

Usage

filter_taxa(physeq, .f, prune = FALSE)

filter_taxa2(physeq, .f)

Functions

• filter_taxa2: Sets prune = TRUE

See Also

phyloseq::filter_taxa tidyseq::transform_sample_counts

Examples

library(phyloseq)
library(tidyseq)
data(GlobalPatterns)
# Filter low prevalence taxa and then convert to proportions
gp.prop <- GlobalPatterns %>%
  filter_taxa2(~ sum(. > 0) > 5) %>%
  transform_sample_counts(~ . / sum(.))

mikemc/tidyseq documentation built on Oct. 27, 2019, 12:46 p.m.