Filter Taxa by Abundance or Prevalence — filter_taxa • microbiomedataset

Filter Taxa by Abundance or Prevalence

Usage

filter_taxa(
  object,
  min_prevalence = NULL,
  min_prevalence_prop = NULL,
  min_abundance = NULL,
  detection = 0
)

Arguments

object: A microbiome_dataset object.
min_prevalence: Minimum prevalence required to keep a taxon.
min_prevalence_prop: Minimum prevalence proportion required to keep a taxon.
min_abundance: Minimum total abundance required to keep a taxon.
detection: Detection threshold used for prevalence.

Value

A microbiome_dataset object.

Examples

data("global_patterns", package = "microbiomedataset")

x <- filter_taxa(
  global_patterns,
  min_prevalence = 5,
  min_abundance = 100
)
dim(x@expression_data)
#> [1] 5646   26