lulu_pq: Lulu reclustering of class 'physeq'

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Lulu reclustering of class physeq

Description

See https://www.nature.com/articles/s41467-017-01312-x for more information on the method.

Usage

lulu_pq(
  physeq,
  nproc = 1,
  id = 0.84,
  vsearchpath = "vsearch",
  verbose = FALSE,
  clean_pq = FALSE,
  keep_temporary_files = FALSE,
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
nproc	(default 1) Set to number of cpus/processors to use for the clustering
id	(default: 0.84) id for –usearch_global.
vsearchpath	(default: vsearch) path to vsearch.
verbose	(logical) if true, print some additional messages.
clean_pq	(logical) if true, empty samples and empty ASV are discarded before clustering.
keep_temporary_files	(logical, default: FALSE) Do we keep temporary files
...	Others args for function lulu()

Details

The version of LULU is a fork of Adrien Taudière (https://github.com/adrientaudiere/lulu) from https://github.com/tobiasgf/lulu

Value

a list of for object

• "new_physeq": The new phyloseq object (class physeq)

• "discrepancy_vector": A vector of discrepancy showing for each taxonomic level the proportion of identic value before and after lulu reclustering. A value of 0.6 stands for 60% of ASV before re-clustering have identical value after re-clustering. In other word, 40% of ASV are assigned to a different taxonomic value. NA value are not counted as discrepancy.

• "res_lulu": A list of the result from the lulu function

• "merged_ASV": the data.frame used to merged ASV

Author(s)

Tobias Guldberg Frøslev [e-mail] & Adrien Taudière [e-mail]

References

• LULU : https://github.com/adrientaudiere/lulu forked from https://github.com/tobiasgf/lulu.

• VSEARCH can be downloaded from https://github.com/torognes/vsearch.

Examples

lulu_pq(data_fungi_sp_known)

MiscMetabar documentation built on May 29, 2024, 10:39 a.m.