blast_to_phyloseq | R Documentation |
refseq
slot of a phyloseq-class
object.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
)
physeq |
(required): a |
seq2search |
(required) path to a fasta file defining the sequences you want to blast against the ASV 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, |
list_no_output_query |
(logical) does the result table include
query sequences for which |
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
|
the blast table
blast_pq()
to use refseq
slot as query sequences
against un custom database.
## Not run:
blastpath <- "...YOUR_PATH_TO_BLAST..."
blast_to_phyloseq(data_fungi,
seq2search = system.file("extdata", "ex.fasta",
package = "MiscMetabar", mustWork = TRUE
),
blastpath = blastpath
)
## End(Not run)
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