percent_unassigned: Find the percentage of reads without a taxon assignment
In ammararuby/MButils: Utility functions for DNA metabarcoding
View source: R/percent_unassigned.R
percent_unassigned R Documentation
Find the percentage of reads without a taxon assignment
Description
Identifies sequence variants with no taxon assignment (*i.e.*,
those for which every column of the taxonomy table is NA). Then,
determines what percentage of overall reads in the dataset correspond to
unidentified reads. This is helpful for determining if the current
reference database for taxonomic assignment is a good fit to the data.
Usage
percent_unassigned(ps, by_sample = FALSE)
Arguments
ps
The phyloseq object to operate on.
by_sample
(Default: FALSE) Whether or not to return the calculations
for the whole object, or broken out by individual samples in the dataset.
Value
The percentage of unmapped reads, either for the overall dataset or
on a per-sample basis.
ammararuby/MButils documentation built on Jan. 29, 2023, 11:13 a.m.
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View source: R/percent_unassigned.R
| percent_unassigned | R Documentation |
Find the percentage of reads without a taxon assignment
Description
Identifies sequence variants with no taxon assignment (*i.e.*, those for which every column of the taxonomy table is NA). Then, determines what percentage of overall reads in the dataset correspond to unidentified reads. This is helpful for determining if the current reference database for taxonomic assignment is a good fit to the data.
Usage
percent_unassigned(ps, by_sample = FALSE)
Arguments
ps |
The phyloseq object to operate on. |
by_sample |
(Default: FALSE) Whether or not to return the calculations for the whole object, or broken out by individual samples in the dataset. |
Value
The percentage of unmapped reads, either for the overall dataset or on a per-sample basis.
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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