reduce_ncbi: Reduce NCBI BLAST results

In fishsciences/metabarcode_utils: Meta-barcoding Utilities

Reduce NCBI BLAST results

Description

Reduces the results of the NCBI BLASTN results.

Usage

reduce_ncbi(
  df,
  keep_cols = c("scientific_name", "common_name", "taxid", "query_cover", "per_ident",
    "accession"),
  accession_keep = c("all", "top"),
  query_threshold = 90,
  thresholds = c(97, 80)
)

Arguments

df	data.frame
keep_cols	vector of column names to keep in the output.
accession_keep	either "all" to keep all accessions, or "top" to only keep the accession with the top per_ident
query_threshold	the threshold of query_coverage. Below this value, a string will be returned.
thresholds	vector of threshold to cut off at. The last will be the lowest per_ident to return.

Value

list of data.frames of reduced rows

Author(s)

Matt Espe

fishsciences/metabarcode_utils documentation built on Feb. 25, 2024, 11:31 a.m.