tagmeFromFasta: Assign taxonomy to an input FASTA file
In gabrielrfernandes/tagme: Taxonomic Assignment of Genetic Markers for Ecology
Description
Usage
Arguments
Value
View source: R/tagmeFromFasta.R
Description
Assign taxonomy to an input FASTA file
Usage
1
tagmeFromFasta(file, db = "./", specificity = 0.8, batch = 50000)
Arguments
file
The FASTA file to be classified. It can be a group of ASV, OTU or Unique sequences.
db
The directory containing the downloaded RDS and TXT files corresponding to your amplicon region. The directory name must end with "/".
specificity
The Specificity that will determine the threshold score for assignment.
batch
The maximum number of sequences to be assigned per batch. Bigger batches demand more memory.
Value
A table containing the taxonomic assignment and the score to each sequence.
gabrielrfernandes/tagme documentation built on Dec. 25, 2021, 1:25 a.m.
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Description Usage Arguments Value
View source: R/tagmeFromFasta.R
Description
Assign taxonomy to an input FASTA file
Usage
1 | tagmeFromFasta(file, db = "./", specificity = 0.8, batch = 50000)
|
Arguments
file |
The FASTA file to be classified. It can be a group of ASV, OTU or Unique sequences. |
db |
The directory containing the downloaded RDS and TXT files corresponding to your amplicon region. The directory name must end with "/". |
specificity |
The Specificity that will determine the threshold score for assignment. |
batch |
The maximum number of sequences to be assigned per batch. Bigger batches demand more memory. |
Value
A table containing the taxonomic assignment and the score to each sequence.
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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