Aggregate a taxon abundance matrix

Given a taxon and a lineage matrix, aggregate taxa belonging to the same higher-level taxon at the specified taxonomic level by summing their abundance.

aggregateTaxa(
  x,
  lineages,
  taxon.level = "class",
  unknown = c(NA, "unclassified"),
  keepUnknown = FALSE,
  keepSumUnknown = FALSE,
  returnLineages = FALSE
)

Arguments

x	an abundance matrix with taxa as rows and samples as columns
lineages	a lineage matrix where row names match row names of taxa; taxa must be provided in the same order as in x; first column gives kingdom, following columns give phylum, class, order, family, genus and species
taxon.level	taxonomic level to which data set is aggregated (kingdom, phylum, class, order, family, genus or species)
unknown	descriptors for unclassified taxa
keepUnknown	keep taxa without higher-level taxon classification; cannot be used together with keepSumUnknown
keepSumUnknown	keep the sum of taxa without higher-level taxon classification on the desired level as last row (row name: sumUnknown)
returnLineages	return lineage matrix for higher-level taxon matrix; if true a list is returned with two elements: abundances and lineages

Value

the aggregated abundance matrix; if returnLineages is true, a list with aggregated abundances and matching lineages

Examples

data("ibd_taxa")
data("ibd_lineages")
ibd_class=aggregateTaxa(x=ibd_taxa,lineages=ibd_lineages)
#> [1] "Number of higher-level taxa: 13"
#> [1] 13  7