vs_search_global {MiscMetabar} | R Documentation |
Search for a list of sequence in a fasta file against physeq reference sequences using vsearch
Description
Usage
vs_search_global(
physeq,
seq2search = NULL,
path_to_fasta = NULL,
vsearchpath = "vsearch",
id = 0.8,
iddef = 0,
keep_temporary_files = FALSE
)
Arguments
physeq |
(required): a |
seq2search |
(required if path_to_fasta is NULL) Either (i) a DNAstringSet object
or (ii) a character vector that will be convert to DNAstringSet using
|
path_to_fasta |
(required if seq2search is NULL) a path to fasta file if seq2search is est to NULL. |
vsearchpath |
(default: vsearch) path to vsearch |
id |
(default: 0.8) id for the option |
iddef |
(default: 0) iddef for the option |
keep_temporary_files |
(logical, default: FALSE) Do we keep temporary files
|
Details
This function is mainly a wrapper of the work of others. Please cite vsearch.
Value
A dataframe with uc results (invisible)
Author(s)
Adrien Taudière
Examples
if (requireNamespace("seqinr")) {
file_dna <- tempfile("dna.fa")
seqinr::write.fasta("GCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTTCAACC",
file = file_dna, names = "seq1"
)
res <- vs_search_global(data_fungi, path_to_fasta = file_dna)
unlink(file_dna)
res[res$identity != "*", ]
clean_pq(subset_taxa(data_fungi, res$identity != "*"))
}