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",
  lulu_exact = FALSE,
  verbose = FALSE,
  clean_pq = TRUE,
  keep_temporary_files = FALSE,
  extra_mumu_args = NULL
)

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
lulu_exact: (logical) If true, use the exact same algorithm as LULU corresponding to the –legacy option of mumu. Need mumu version >= v1.1.0
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
extra_mumu_args: (character, default: NULL) Additional arguments passed on to mumu command line. See man mumu into bash for details. Major args are --minimum_match, --minimum_ratio_type, --minimum_ratio, --minimum_relative_cooccurence and --threads

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) { # \dontrun{
ntaxa(data_fungi_sp_known)
ntaxa(mumu_pq(data_fungi_sp_known)$new_physeq)
ntaxa(mumu_pq(data_fungi_sp_known, extra_mumu_args = "--minimum_match 90")$new_physeq)
} # }

MUMU reclustering of class `physeq`