findnonmissing: Identify Non-Missing Taxonomic Labels
In HPCBio/plotly_microbiome: Helper Functions for Plotly Graphs in Microbiome Work
findnonmissing R Documentation
Identify Non-Missing Taxonomic Labels
Description
In various taxonomic databases and pipelines, unknown or missing
taxonomic labels may be indicated in a variety of ways, such as
missing data, "unclassified", "uncultured", etc. This function
identifies all of these that I have encountered so far.
Usage
findnonmissing(x)
Arguments
x
A character vector of taxonomic labels, for example a single
column of the tax_table slot of a phyloseq object.
Details
The following values will result in output of FALSE.
-
NA
An empty string.
The words “unclassified”, “unidentified”,
“uncultured”, “unknown”, or “metagenome” anywhere in the
string, in any case.
Values equal to “human_gut.”
Value
A logical vector, with TRUE if the taxonomic label reflects a
taxonomic identity, and FALSE if it should be considered missing.
Author(s)
Lindsay V. Clark
Examples
findnonmissing(c("Streptococcus", "Blautia", "Horse metagenome", NA))
HPCBio/plotly_microbiome documentation built on May 9, 2022, 11:37 p.m.
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| findnonmissing | R Documentation |
Identify Non-Missing Taxonomic Labels
Description
In various taxonomic databases and pipelines, unknown or missing taxonomic labels may be indicated in a variety of ways, such as missing data, "unclassified", "uncultured", etc. This function identifies all of these that I have encountered so far.
Usage
findnonmissing(x)
Arguments
x |
A character vector of taxonomic labels, for example a single
column of the |
Details
The following values will result in output of FALSE.
-
NA An empty string.
The words “unclassified”, “unidentified”, “uncultured”, “unknown”, or “metagenome” anywhere in the string, in any case.
Values equal to “human_gut.”
Value
A logical vector, with TRUE if the taxonomic label reflects a
taxonomic identity, and FALSE if it should be considered missing.
Author(s)
Lindsay V. Clark
Examples
findnonmissing(c("Streptococcus", "Blautia", "Horse metagenome", NA))
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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