filter_data: Filter out low abundance taxa

In kimberlyroche/ROL: What the package does (short line)

Description

Filter out low abundance taxa

Usage

filter_data(
  data,
  tax_level = NULL,
  count_threshold = 5,
  sample_threshold = 0.2
)

Arguments

data	a phyloseq object
tax_level	taxonomic level at which data have been agglomerated
count_threshold	minimum count at which a taxon must be observed
sample_threshold	minimum proportion of samples within each host at which a taxon must be observed at the level specified by count_threshold

Details

Together count_threshold and sample_threshold specify a minimum representation for a taxon. Taxa below these observed thresholds will be grouped together into a category "Collapsed".

Value

phyloseq object

Examples

filtered_data <- filter_data(data, count_threshold=5, sample_threshold=0.2)

kimberlyroche/ROL documentation built on Dec. 10, 2020, 2:18 a.m.