filter_asv_blast: Filter undesirable taxa using blast against a custom...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Filter undesirable taxa using blast against a custom database.

Description

Use the blast software.

Usage

filter_asv_blast(
  physeq,
  fasta_for_db = NULL,
  database = NULL,
  clean_pq = TRUE,
  add_info_to_taxtable = TRUE,
  id_filter = 90,
  bit_score_filter = 50,
  min_cover_filter = 50,
  e_value_filter = 1e-30,
  ...
)

filter_taxa_blast(
  physeq,
  fasta_for_db = NULL,
  database = NULL,
  clean_pq = TRUE,
  add_info_to_taxtable = TRUE,
  id_filter = 90,
  bit_score_filter = 50,
  min_cover_filter = 50,
  e_value_filter = 1e-30,
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
fasta_for_db	path to a fasta file to make the blast database
database	path to a blast database
clean_pq	(logical) If set to TRUE, empty samples and empty taxa (ASV, OTU) are discarded after filtering.
add_info_to_taxtable	(logical, default TRUE) Does the blast information are added to the taxtable ?
id_filter	(default: 90) cut of in identity percent to keep result
bit_score_filter	(default: 50) cut of in bit score to keep result The higher the bit-score, the better the sequence similarity. The bit-score is the requires size of a sequence database in which the current match could be found just by chance. The bit-score is a log2 scaled and normalized raw-score. Each increase by one doubles the required database size (2bit-score).
min_cover_filter	(default: 50) cut of in query cover (%) to keep result
e_value_filter	(default: 1e-30) cut of in e-value (%) to keep result The BLAST E-value is the number of expected hits of similar quality (score) that could be found just by chance.
...	Others options for the blast_pq() function. See ?blast_pq. Note that params unique_per_seq must be lft to TRUE and score_filter must be left to FALSE.

Value

A new phyloseq-class object.

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.