Skip to contents

Assign taxonomy using LCA à la stampa

Source: R/vsearch.R
assign_vsearch_lca.Rd

lifecycle-experimental

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

Usage

assign_vsearch_lca(
  physeq = NULL,
  seq2search = NULL,
  ref_fasta = NULL,
  behavior = "return_matrix",
  vsearchpath = "vsearch",
  clean_pq = TRUE,
  taxo_rank = c("K", "P", "C", "O", "F", "G", "S"),
  nproc = 1,
  suffix = "",
  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 = ""
)

Arguments

physeq

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

A DNAStringSet object of sequences to search for.

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

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.

taxo_rank

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 taxo_rank algorithm is used without suffix.

id

(Int. [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_cutoof. 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

Other arguments to be passed on to vsearch usearch_global cmd.

Value

See param behavior

Details

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

See also

assign_sintax(), add_new_taxonomy_pq()

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
)
#> Cleaning suppress 0 taxa and 0 samples.
# }