View source: R/dada_phyloseq.R
mumu_pq | R Documentation |
physeq
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
mumu_pq(
physeq,
nproc = 1,
id = 0.84,
vsearchpath = "vsearch",
mumupath = "mumu",
verbose = FALSE,
clean_pq = TRUE,
keep_temporary_files = FALSE
)
physeq |
(required): a |
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 |
This function is mainly a wrapper of the work of others. Please cite mumu and lulu if you use this function for your work.
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.
Frédéric Mahé & Adrien Taudière adrien.taudiere@zaclys.net
VSEARCH can be downloaded from https://github.com/torognes/vsearch.
lulu_pq()
## Not run:
mumu_pq(data_fungi_sp_known)
## End(Not run)
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