Merge taxa in x into a smaller set of taxa defined by the vector group.
Taxa whose value in group is NA will be dropped. New taxa will be named
according to the most abundant taxon in each group (phyloseq and
otu_table objects) or the first taxon in each group (all other phyloseq
component objects).
merge_taxa_vec(x, group, reorder = FALSE, tax_adjust = 1L) # S4 method for phyloseq merge_taxa_vec(x, group, reorder = FALSE, tax_adjust = 1L) # S4 method for otu_table merge_taxa_vec(x, group, reorder = FALSE) # S4 method for taxonomyTable merge_taxa_vec(x, group, reorder = FALSE, tax_adjust = 1L) # S4 method for phylo merge_taxa_vec(x, group) # S4 method for XStringSet merge_taxa_vec(x, group, reorder = FALSE)
| x | A phyloseq object or component object |
|---|---|
| group | A vector with one element for each taxon in |
| reorder | Logical specifying whether to reorder the taxa by their
|
| tax_adjust | 0: no adjustment; 1: phyloseq-compatible adjustment; 2: conservative adjustment |
If x is a phyloseq object with a phylogenetic tree, then the new taxa will
be ordered as they are in the tree. Otherwise, the taxa order can be
controlled by the reorder argument, which behaves like the reorder
argument in base::rowsum(). reorder = FALSE will keep taxa in
the original order determined by when the member of each group first appears
in taxa_names(x); reorder = TRUE will order new taxa according to their
corresponding value in group.
The tax_adjust argument controls the handling of taxonomic disagreements
within groups. Setting tax_adjust == 0 causes no adjustment; the taxonomy
of the new group is set to the archetype taxon (see below). Otherwise,
disagreements within a group at a given rank cause the values at lower ranks
to be set to NA. If tax_adjust == 1 (the default), then a rank where all
taxa in the group are already NA is not counted as a disagreement, and lower
ranks may be kept if the taxa agree. This corresponds to the original
phyloseq behavior. If tax_adjust == 2, then these NAs are treated as a
disagreement; all ranks are set to NA after the first disagreement or NA.
Merging functions that use this function: tax_glom(), tip_glom(),
tree_glom()
if (FALSE) { # Create 97% OTUs from a phyloseq object with reference sequences # Assume ps is a phyloseq object with refseq slot dna <- refseq(ps) nproc <- 1 # Increase to use multiple processors aln <- DECIPHER::AlignSeqs(dna, processors = nproc) d <- DECIPHER::DistanceMatrix(aln, processors = nproc) clusters <- DECIPHER::IdClusters( d, method = "complete", cutoff = 0.03, processors = nproc ) ps0 <- merge_taxa_vec( ps, group = clusters$cluster, ) }