Assign taxonomy using LCA

Please cite Vsearch and stampa if you use this function to assign taxonomy.

If top_hits_only is TRUE, the algorithm is the one of stampa.
If top_hits_only is FALSE and vote_algorithm is NULL, you need to carefully define maxaccept, id and lca_cutoff parameters. The algorithm is internal to vsearch using the lcaout output.
If top_hits_only is FALSE and vote_algorithm is not NULL, conflict among the list of taxonomic assignations is resolve using the function resolve_vector_ranks(). The possible values for vote_algorithm are "consensus", "rel_majority", "abs_majority" and "unanimity". See resolve_vector_ranks() for more details.

Usage

assign_vsearch_lca(
  physeq = NULL,
  ref_fasta = NULL,
  seq2search = NULL,
  behavior = c("return_matrix", "add_to_phyloseq", "return_cmd"),
  vsearchpath = "vsearch",
  clean_pq = TRUE,
  taxa_ranks = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  nproc = 1,
  suffix = "_sintax",
  id = 0.5,
  lca_cutoff = 1,
  maxrejects = 32,
  top_hits_only = TRUE,
  maxaccepts = 0,
  keep_temporary_files = FALSE,
  verbose = TRUE,
  temporary_fasta_file = "temp.fasta",
  cmd_args = "",
  too_few = "align_start",
  vote_algorithm = NULL,
  nb_voting = NULL,
  strict = FALSE,
  nb_agree_threshold = 1,
  preference_index = NULL,
  collapse_string = "/",
  replace_collapsed_rank_by_NA = TRUE,
  simplify_taxo = TRUE,
  keep_vsearch_score = FALSE
)

Arguments

physeq

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

ref_fasta

(required) A link to a database in vsearch format The reference database must contain taxonomic information in the header of each sequence in the form of a string starting with ";tax=" and followed by a comma-separated list of up to nine taxonomic identifiers. Each taxonomic identifier must start with an indication of the rank by one of the letters d (for domain) k (kingdom), p (phylum), c (class), o (order), f (family), g (genus), s (species), or t (strain). The letter is followed by a colon (:) and the name of that rank. Commas and semicolons are not allowed in the name of the rank. Non-ascii characters should be avoided in the names.

Example:

\>X80725_S000004313;tax=d:Bacteria,p:Proteobacteria,c:Gammaproteobacteria,o:Enterobacteriales,f:Enterobacteriaceae,g:Escherichia/Shigella,s:Escherichia_coli,t:str._K-12_substr._MG1655

seq2search

A DNAStringSet object of sequences to search for. Replace the physeq object.

behavior

Either "return_matrix" (default), "return_cmd", 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.
"return_cmd" return the command to run without running it.
"add_to_phyloseq" return a phyloseq object with amended slot @taxtable. Only available if using physeq input and not seq2search input.

vsearchpath

(default: "vsearch") path to vsearch

clean_pq

(logical, default TRUE) If set to TRUE, empty samples and empty ASV are discarded before clustering.

taxa_ranks

A list with the name of the taxonomic rank present in ref_fasta

nproc

(int, default: 1) Set to number of cpus/processors to use

suffix

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

id

(Float [0:1] default 0.5). Default value is based on stampa. See Vsearch Manual for parameter --id

lca_cutoff

(int, default 1). Fraction of matching hits required for the last common ancestor (LCA) output. For example, a value of 0.9 imply that if less than 10% of assigned species are not congruent the taxonomy is filled. Default value is based on stampa. See Vsearch Manual for parameter --lca_cutoff

Text from vsearch manual : "Adjust the fraction of matching hits required for the last common ancestor (LCA) output with the –lcaout option during searches. The default value is 1.0 which requires all hits to match at each taxonomic rank for that rank to be included. If a lower cutoff value is used, e.g. 0.95, a small fraction of non-matching hits are allowed while that rank will still be reported. The argument to this option must be larger than 0.5, but not larger than 1.0"

maxrejects

(int, default: 32) Maximum number of non-matching target sequences to consider before stopping the search for a given query. Default value is based on stampa See Vsearch Manual for parameter --maxrejects.

top_hits_only

(Logical, default TRUE) Only the top hits with an equally high percentage of identity between the query and database sequence sets are written to the output. If you set top_hits_only you may need to set a lower maxaccepts and/or lca_cutoff. Default value is based on stampa See Vsearch Manual for parameter --top_hits_only

maxaccepts

(int, default: 0) Default value is based on stampa. Maximum number of matching target sequences to accept before stopping the search for a given query. See Vsearch Manual for parameter --maxaccepts

keep_temporary_files

(logical, default: FALSE) Do we keep temporary files?

temporary_fasta_file (default "temp.fasta") : the fasta file from physeq or seq2search
"out_lca.txt" : see Vsearch Manual for parameter –lcaout
"userout.txt" : see Vsearch Manual for parameter –userout

verbose

(logical). If TRUE, print additional information.

temporary_fasta_file

Name of the temporary fasta file. Only useful with keep_temporary_files = TRUE.

cmd_args

Additional arguments passed on to vsearch usearch_global cmd.

too_few

(default value "align_start") see tidyr::separate_wider_delim()

vote_algorithm

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

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.

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_vsearch_score

(Logical, default FALSE). If TRUE, the mean and sd of id score are stored in the tax_table.

Value

See param behavior

Details

This function is mainly a wrapper of the work of others. Please cite vsearch and stampa

Author

Adrien Taudière

Examples

# \donttest{
data_fungi_mini_new <- assign_vsearch_lca(data_fungi_mini,
  ref_fasta = system.file("extdata", "mini_UNITE_fungi.fasta.gz", package = "MiscMetabar"),
  lca_cutoff = 0.9, behavior = "add_to_phyloseq"
)

data_fungi_mini_new2 <- assign_vsearch_lca(data_fungi_mini,
  ref_fasta = system.file("extdata", "mini_UNITE_fungi.fasta.gz", package = "MiscMetabar"),
  id = 0.8, behavior = "add_to_phyloseq", top_hits_only = FALSE
)

data_fungi_mini_new3 <- assign_vsearch_lca(data_fungi_mini,
  ref_fasta = system.file("extdata", "mini_UNITE_fungi.fasta.gz", package = "MiscMetabar"),
  id = 0.5, behavior = "add_to_phyloseq", top_hits_only = FALSE, vote_algorithm = "rel_majority"
)
# }

Usage

Arguments

Value

Details

See also

Author

Examples