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Assign taxonomy using blastn algorithm and the blast software

Source: R/blast.R
assign_blastn.Rd

lifecycle-experimental

Use the blast software.

Usage

assign_blastn(
  physeq,
  ref_fasta = NULL,
  database = NULL,
  blastpath = NULL,
  behavior = c("return_matrix", "add_to_phyloseq"),
  method = c("vote", "top-hit"),
  suffix = "_blastn",
  min_id = 95,
  min_bit_score = 50,
  min_cover = 95,
  min_e_value = 1e-30,
  nb_voting = NULL,
  column_names = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  vote_algorithm = c("consensus", "rel_majority", "abs_majority", "unanimity"),
  strict = FALSE,
  nb_agree_threshold = 1,
  preference_index = NULL,
  collapse_string = "/",
  replace_collapsed_rank_by_NA = TRUE,
  simplify_taxo = TRUE,
  keep_blast_metrics = FALSE,
  ...
)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

ref_fasta

Either a DNAStringSet object or a path to a fasta file to make the blast database. It must be in sintax format. See assign_sintax().

database

path to a blast database. Only used if ref_fasta is not set.

blastpath

path to blast program.

behavior

Either "return_matrix" (default), or "add_to_phyloseq":

  • "return_matrix" return a list of two matrix with taxonomic value in the first element of the list and bootstrap value in the second one.

  • "add_to_phyloseq" return a phyloseq object with amended slot @taxtable. Only available if using physeq input and not seq2search input.

method

(One of "vote" or "top-hit"). If top-hit, only the better match is used to assign taxonomy. If vote, the algorithm takes all (or nb_voting if nb_voting is not null) select assignation and resolve the conflict using the function resolve_vector_ranks().

suffix

(character) The suffix to name the new columns. If set to "" (the default), the taxa_ranks algorithm is used without suffix.

min_id

(default: 95) the identity percent to take into account a references taxa

min_bit_score

(default: 50) the minimum bit score to take into account a references taxa

min_cover

(default: 50) cut of in query cover (%) to keep result

min_e_value

(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.

nb_voting

(Int, default NULL). The number of taxa to keep before apply a vote to resolve conflict. If NULL all taxa passing the filters (min_id, min_bit_score, min_cover and min_e_value) are selected.

column_names

A vector of names for taxonomic ranks. Must correspond to names in the ref_fasta files.

vote_algorithm

the method to vote among "consensus", "rel_majority", "abs_majority" and "unanimity". See resolve_vector_ranks() for more details.

strict

(Logical, default FALSE). See resolve_vector_ranks() for more details.

nb_agree_threshold

See resolve_vector_ranks() for more details.

preference_index

See resolve_vector_ranks() for more details.

collapse_string

See resolve_vector_ranks() for more details.

replace_collapsed_rank_by_NA

(Logical, default TRUE) See resolve_vector_ranks() for more details.

simplify_taxo

(logical default TRUE). Do we apply the function simplify_taxo() to the phyloseq object?

keep_blast_metrics

(Logical, default FALSE). If TRUE, the blast metrics ("Query seq. length", "Taxa seq. length", "Alignment length", "% id. match", "e-value", "bit score" and "Query cover") are stored in the tax_table.

...

Additional arguments passed on to blast_pq()

Value

  • If behavior == "return_matrix" :

    • If method = "top-hit" a matrix of taxonomic assignation

    • If method = "vote", a list of two matrix, the first is the raw taxonomic assignation (before vote). The second one is the taxonomic assignation in which conflicts are resolved using vote.

  • If behavior == "add_to_phyloseq", return a new phyloseq object

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
ref_fasta <- Biostrings::readDNAStringSet(system.file("extdata",
  "mini_UNITE_fungi.fasta.gz",
  package = "MiscMetabar", mustWork = TRUE
))

# assign_blastn(data_fungi_mini, ref_fasta = ref_fasta) # error because not
# enough sequences in db so none blast query passed the filters.
# So we used low score filter hereafter.

mat <- assign_blastn(data_fungi_mini,
  ref_fasta = ref_fasta,
  method = "top-hit", min_id = 70, min_e_value = 1e-3, min_cover = 50,
  min_bit_score = 20
)
head(mat)

assign_blastn(data_fungi_mini,
  ref_fasta = ref_fasta, method = "vote",
  vote_algorithm = "rel_majority", min_id = 90, min_cover = 50,
  behavior = "add_to_phyloseq"
)@tax_table

assign_blastn(data_fungi_mini,
  ref_fasta = ref_fasta, method = "vote",
  vote_algorithm = "consensus", replace_collapsed_rank_by_NA = FALSE,
  min_id = 90, min_cover = 50, behavior = "add_to_phyloseq"
)@tax_table
} # }