prune_data: Description TBD
In kimberlyroche/rulesoflife:
prune_data R Documentation
Description TBD
Description
Description TBD
Usage
prune_data(seq_similarity_threshold = 0.99)
Arguments
seq_similarity_threshold
percent upper limit on sequence similarity;
for ASV pairs strictly more similar than this, the less abundant partner in
the pair will be removed from the data as it's likely these partners ID the
same taxon
host_sample_min
minimum sample number for host inclusion in the
filtered data set
count_threshold
minimum count for taxon inclusion in the filtered data
set
sample_threshold
minimum proportion of samples within each host at
which a taxon must be observed at or above count_threshold
Details
Typically, ASV pairs with >99
Value
phyloseq object
kimberlyroche/rulesoflife documentation built on May 7, 2023, 11:08 a.m.
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| prune_data | R Documentation |
Description TBD
Description
Description TBD
Usage
prune_data(seq_similarity_threshold = 0.99)
Arguments
seq_similarity_threshold |
percent upper limit on sequence similarity; for ASV pairs strictly more similar than this, the less abundant partner in the pair will be removed from the data as it's likely these partners ID the same taxon |
host_sample_min |
minimum sample number for host inclusion in the filtered data set |
count_threshold |
minimum count for taxon inclusion in the filtered data set |
sample_threshold |
minimum proportion of samples within each host at which a taxon must be observed at or above count_threshold |
Details
Typically, ASV pairs with >99
Value
phyloseq object
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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