condenseTaxa {taxonomizr} | R Documentation |
Condense multiple taxonomic assignments to their most recent common branch
Description
Take a table of taxonomic assignments, e.g. assignments from hits to a read, and condense it to a single vector with NAs where there are disagreements between the hits.
Usage
condenseTaxa(taxaTable, groupings = rep(1, nrow(taxaTable)))
Arguments
taxaTable |
a matrix or data.frame with hits on the rows and various levels of taxonomy in the columns |
groupings |
a vector of groups e.g. read queries to condense taxa within |
Value
a matrix with ncol(taxaTable)
taxonomy columns with a row for each unique id (labelled on rownames) with NAs where there was not complete agreement for an id
Examples
taxas<-matrix(c(
'a','b','c','e',
'a','b','d','e'
),nrow=2,byrow=TRUE)
condenseTaxa(taxas)
condenseTaxa(taxas[c(1,2,2),],c(1,1,2))
[Package taxonomizr version 0.10.6 Index]