Runs the taxonomy lookup, duplicate removal, outlier detection, and taxonomic filtering that sq.curate needs regardless of whether the input sequences come from disk (folder) or from an in-memory sqs.object. Both entry points in sq.curate build a named list of DNAbin sequences (fastaSeqs) and hand it here, then take care of their own export step (writing FASTA/CSV files, or returning a list).
Usage
curate.sequences.core(
fastaSeqs,
fileNames,
filterTaxonomicCriteria,
database,
kingdom,
removeOutliers,
minSeqs,
threshold,
ranks
)Arguments
- fastaSeqs
A named list of DNAbin sequences, one element per gene file.
- fileNames
The file (or gene) names associated with fastaSeqs, used to track which sequences came from which source.
- filterTaxonomicCriteria
See
sq.curate.- database
See
sq.curate.- kingdom
See
sq.curate.- removeOutliers
See
sq.curate.- minSeqs
See
sq.curate.- threshold
See
sq.curate.- ranks
See
sq.curate.