A wrapper of DECIPHER::LearnTaxa() — learn

This function is basically a wrapper of functions DECIPHER::LearnTaxa(), please cite the DECIPHER package if you use this function.

Usage

learn_idtaxa(
  fasta_for_training,
  output_Rdata = NULL,
  output_path_only = FALSE,
  unite = FALSE,
  ...
)

Arguments

fasta_for_training

A fasta file (can be gzip) to train the trainingSet using the function learn_idtaxa(). Only used if trainingSet is NULL.

The reference database must contain taxonomic information in the header of each sequence in the form of a string starting with ";tax=" and followed by a comma-separated list of up to nine taxonomic identifiers.

The only exception is if unite=TRUE. In that case the UNITE taxonomy is automatically formatted.

output_Rdata

A vector naming the path to an output Rdata file. If left to NULL, no Rdata file is written.

output_path_only

(logical, default FALSE). If TRUE, the function return only the path to the output_Rdata file. Note that output_Rdata must be set.

unite

(logical, default FALSE). If set to TRUE, the fasta_for_training file is formatted from UNITE format to sintax one, needed in fasta_for_training. Only used if trainingSet is NULL.

...

Additional arguments passed on to DECIPHER::LearnTaxa()

Value

Either a Taxa Train object (see DECIPHER::LearnTaxa()) or, if output_path_only is TRUE, a vector indicating the path to the output training object.

Details

This function is mainly a wrapper of the work of others. Please make a reference to DECIPHER::LearnTaxa() if you use this function.

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
training_mini_UNITE_fungi <-
  learn_idtaxa(fasta_for_training = system.file("extdata",
    "mini_UNITE_fungi.fasta.gz",
    package = "MiscMetabar"
  ))
plot(training_mini_UNITE_fungi)

training_100sp_UNITE <-
  learn_idtaxa(
    fasta_for_training = system.file("extdata",
      "100_sp_UNITE_sh_general_release_dynamic.fasta",
      package = "MiscMetabar"
    ),
    unite = TRUE
  )

plot(training_100sp_UNITE)
} # }