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

Source: R/blast.R
blast_to_phyloseq.Rd

lifecycle-maturing

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.

(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

if (FALSE) { # \dontrun{

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