asgntax: Taxonomy assignment based on external reference database in...
In peterolah001/BiMiCo: Biomap Microbiome Core methods
asgntax R Documentation
Taxonomy assignment based on external reference database in BiMiCo pipeline
Description
Generates taxonomic assignment of ASV sequences, given an ASV table generated by BiMiCo and an external taxonomic reference database compatible with DADA2 'assignTaxonomy' function. Currently Greengenes v13.5 is provided with the package.
Usage
asgntax(asvtab, taxdat, revcomp = T, mtthread)
Arguments
asvtab
(Required) ASV table object (of class matrix) created by the 'std_(454/Illum)_ASVtab' function (ASVs in rows, samples in columns)
taxdat
(Required) Path to taxonomy database file compatible with DADA2 'assignTaxonomy' function
revcomp
(Optional) Boolean, whether to check reverse complement of reference sequence. Default=T
mtthread
(Required) Boolean, enables multithreading (not recommended in Rstudio)
Examples
asgntax()
peterolah001/BiMiCo documentation built on April 24, 2023, 3:35 a.m.
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| asgntax | R Documentation |
Taxonomy assignment based on external reference database in BiMiCo pipeline
Description
Generates taxonomic assignment of ASV sequences, given an ASV table generated by BiMiCo and an external taxonomic reference database compatible with DADA2 'assignTaxonomy' function. Currently Greengenes v13.5 is provided with the package.
Usage
asgntax(asvtab, taxdat, revcomp = T, mtthread)
Arguments
asvtab |
(Required) ASV table object (of class matrix) created by the 'std_(454/Illum)_ASVtab' function (ASVs in rows, samples in columns) |
taxdat |
(Required) Path to taxonomy database file compatible with DADA2 'assignTaxonomy' function |
revcomp |
(Optional) Boolean, whether to check reverse complement of reference sequence. Default=T |
mtthread |
(Required) Boolean, enables multithreading (not recommended in Rstudio) |
Examples
asgntax()
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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