blast_to_phyloseq: Blast some sequence against 'refseq' slot of a...

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Blast some sequence against refseq slot of a phyloseq-class object.

Description

Use the blast software.

Usage

blast_to_phyloseq(
  physeq,
  seq2search,
  blastpath = NULL,
  id_cut = 90,
  bit_score_cut = 50,
  min_cover_cut = 50,
  e_value_cut = 1e-30,
  unique_per_seq = FALSE,
  score_filter = TRUE,
  list_no_output_query = FALSE,
  args_makedb = NULL,
  args_blastn = NULL,
  nproc = 1,
  keep_temporary_files = FALSE
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
seq2search	(required) path to a fasta file defining the sequences you want to blast against the taxa (ASV, OTU) sequences from the physeq object.
blastpath	path to blast program
id_cut	(default: 90) cut of in identity percent to keep result
bit_score_cut	(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_cut	(default: 50) cut of in query cover (%) to keep result
e_value_cut	(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.
unique_per_seq	(logical, default FALSE) if TRUE only return the better match (higher bit score) for each sequence
score_filter	(logical, default TRUE) does results are filter by score? If FALSE, id_cut,bit_score_cut, e_value_cut and min_cover_cut are ignored
list_no_output_query	(logical) does the result table include query sequences for which blastn does not find any correspondence?
args_makedb	Additional parameters parse to makeblastdb command
args_blastn	Additional parameters parse to blastn command
nproc	(default: 1) Set to number of cpus/processors to use for blast (args -num_threads for blastn command)
keep_temporary_files	(logical, default: FALSE) Do we keep temporary files db.fasta (refseq transformed into a database) dbase list of files (output of blastn) blast_result.txt the summary result of blastn using ⁠-outfmt "6 qseqid qlen sseqid slen length pident evalue bitscore qcovs"⁠

Value

the blast table

See Also

blast_pq() to use refseq slot as query sequences against un custom database.

Examples

## Not run: 

blastpath <- "...YOUR_PATH_TO_BLAST..."
blast_to_phyloseq(data_fungi,
  seq2search = system.file("extdata", "ex.fasta",
    package = "MiscMetabar", mustWork = TRUE
  ),
  blastpath = blastpath
)

## End(Not run)

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.