aggregate_abund: Aggregate OTUs to a specific taxonomic level

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

Aggregate OTUs to a specific taxonomic level

Description

Sums up all OTU read counts at the chosen taxonomic level. Used internally in many ampvis2 functions, but can also be used separately for custom purposes.

Usage

aggregate_abund(
  abund,
  tax,
  tax_aggregate = "OTU",
  tax_add = NULL,
  calcSums = TRUE,
  format = "long"
)

Arguments

abund	The OTU abundance table from an ampvis2 object (ampvis2obj$abund)
tax	The OTU abundance table from an ampvis2 object (ampvis2obj$tax)
tax_aggregate	Aggregate (sum) OTU's to a specific taxonomic level. (default: "OTU")
tax_add	Add additional (higher) taxonomic levels to the taxonomy string. The OTU's will be aggregated to whichever level of the tax_aggregate and tax_add vectors is the lowest. (default: NULL)
calcSums	Whether to include the sums of read counts for each sample and taxonomic group. (default: TRUE)
format	Output format, "long" or "abund". "abund" corresponds to that of a read counts table with samples as columns and the aggregated taxa as rows.

Value

A data.table.

Author(s)

Kasper Skytte Andersen [e-mail]

Examples

data("AalborgWWTPs")
aggregated <- aggregate_abund(
  AalborgWWTPs$abund,
  AalborgWWTPs$tax,
  tax_aggregate = "Genus",
  tax_add = "Phylum",
  format = "long",
  calcSums = TRUE
)
aggregated

MadsAlbertsen/ampvis2 documentation built on Jan. 28, 2024, 7:12 a.m.