bin_taxonomy: Bin ASV count table at a specified level of taxonomic...

In mselensky/bngal: Biological Network Graphing and Learning

Bin ASV count table at a specified level of taxonomic classification

Description

This is the primary data formatting function of most bngal pipelines, including the first step of network analysis.

Usage

bin_taxonomy(
  asv.table,
  meta.data,
  tax.level,
  remove.singletons = TRUE,
  cutoff.val,
  direction,
  compositional = TRUE
)

Arguments

asv.table	ASV count table named by Silva-138 L7 taxonomies. Ideally rarefied and quality filtered as necessary, though this script automatically removes singletons in the dataset. First column must be named "sample-id" and must contain unique identifiers.
meta.data	Sample metadata corresponding to asv.table.
tax.level	Level of taxonomic classification at which to calculate relative abundance.
remove.singletons	Optional Drop singleton ASV observations from the dataset. Default = TRUE
cutoff.val	Optional Cutoff value for ASVs that comprise more or less than this fraction of a sample's community (values 0 to 1 accepted). Required if 'direction' specified.
direction	Optional Return binned data 'lessThan' or 'greaterThan' than cutoff.val. Required if 'cutoff.val' specified.
compositional	Optional Determines whether output returns relative abundance (TRUE) or binned count data (FALSE). Default = TRUE.

Examples

# return long-form class-level count data
bin_taxonomy(asv_table, metadata, "class", compositional = FALSE)

# return long-form family-level relative abundance data
bin_taxonomy(asv_table, metadata, "family")

mselensky/bngal documentation built on June 3, 2024, 6:27 a.m.