View source: R/dada_phyloseq.R
lulu_pq | R Documentation |
physeq
See https://www.nature.com/articles/s41467-017-01312-x for more information on the method.
lulu_pq(
physeq,
nproc = 1,
id = 0.84,
vsearchpath = "vsearch",
verbose = FALSE,
clean_pq = FALSE,
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. |
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 |
The version of LULU is a fork of Adrien Taudière (https://github.com/adrientaudiere/lulu) from https://github.com/tobiasgf/lulu
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
Tobias Guldberg Frøslev tobiasgf@snm.ku.dk & Adrien Taudière adrien.taudiere@zaclys.net
LULU : https://github.com/adrientaudiere/lulu forked from https://github.com/tobiasgf/lulu.
VSEARCH can be downloaded from https://github.com/torognes/vsearch.
lulu_pq(data_fungi_sp_known)
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