MUMU reclustering of class physeq — mumu

See https://www.nature.com/articles/s41467-017-01312-x for more information on the original method LULU. This is a wrapper of mumu a C++ re-implementation of LULU by Frédéric Mahé

Usage

mumu_pq(
  physeq,
  nproc = 1,
  id = 0.84,
  vsearchpath = "vsearch",
  mumupath = "mumu",
  verbose = FALSE,
  clean_pq = TRUE,
  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.
mumupath: path to mumu. See mumu for installation instruction
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

Value

a list of for object

"new_physeq": The new phyloseq object (class physeq)
"mumu_results": The log file of the mumu software. Run man mumu into bash to obtain details about columns' signification.

Details

This function is mainly a wrapper of the work of others. Please cite mumu and lulu if you use this function for your work.

References

MUMU: https://github.com/frederic-mahe/mumu
VSEARCH can be downloaded from https://github.com/torognes/vsearch.

Author

Frédéric Mahé & Adrien Taudière adrien.taudiere@zaclys.net

Examples

if (FALSE) {
mumu_pq(data_fungi_sp_known)
}