idtax2df: Converts outputs of DECIPHER's idtaxa algorithm into a dataframe compatible with the algorithms used in ensembleTax.

Description

Converts outputs of DECIPHER's idtaxa algorithm into a dataframe compatible with the algorithms used in ensembleTax.

Usage

idtax2df(
  tt,
  db = "pr2",
  ranks = NULL,
  boot = 0,
  rubric = NULL,
  return.conf = FALSE
)

Arguments

The taxonomy table output by DECIPHER's idtaxa algorithm

The database you ran idtaxa against. Either "pr2", "silva", "rdp", or "gg" are supported.

ranks

NULL, or a character vector of column names if db is set to NULL

boot

The bootstrap threshold below which taxonomic assignments should be set to NA. This can also be done with DECIPHER's idtaxa but is included here for convenience.

rubric

a DNAStringSet (see Biostrings package) with ASV sequences named by your preferred ASV identifier. Both the ASV sequence and identifier will be merged with the output dataframe. If NULL, ASV-identifying data is not included in the output dataframe.

return.conf

If TRUE, returns a list where the first element is your formatted taxonomy table and the second element is a dataframe of bootstrap confidence values. If FALSE, your formatted taxonomy table is returned as a dataframe.

Value

a dataframe formatted for use with taxmapper and/or ensembleTax

Details

For consistency with DADA2's assignTaxonomy function, when used with Silva, RDP, or GreenGenes it subsamples the ranks c("domain", "phylum", "class", "order", "family", "genus"). Set db = NULL and supply ranks for databases that aren't directly supported. The output taxonomy table is sorted by the ASV-identifying data supplied in the rubric.

CAUTION: the idtaxa algorithm does not return any ASV-identifying data in its output "taxon" object. The elements of tt should thus be supplied in the same order as the elements in rubric. This will typically be the case so long as there is no tampering with the rubric or taxon object in between implementing idtaxa and their use here.

Examples

Run this code

# NOT RUN {
data("idtax.pr2.sample")
data("rubric.sample")
head(idtax.pr2.sample)
head(rubric.sample)
df <- idtax2df(tt = idtax.pr2.sample, db = "pr2", ranks = NULL, boot = 0,
rubric = NULL, return.conf = FALSE)
head(df)
df <- idtax2df(tt = idtax.pr2.sample, db = "pr2", ranks = NULL, boot = 0,
rubric = rubric.sample, return.conf = FALSE)
head(df)
df <- idtax2df(tt = idtax.pr2.sample, db = "pr2", ranks = NULL, boot = 60,
rubric = rubric.sample, return.conf = FALSE)
head(df)
df <- idtax2df(tt = idtax.pr2.sample, db = "pr2", ranks = NULL, boot = 60,
rubric = rubric.sample, return.conf = TRUE)
head(df)

# }