filter_asv_blast | R Documentation |
filter_asv_blast(
physeq,
fasta_for_db = NULL,
database = NULL,
clean_pq = TRUE,
add_info_to_taxtable = TRUE,
id_filter = 90,
bit_score_filter = 50,
min_cover_filter = 50,
e_value_filter = 1e-30,
...
)
physeq |
(required): a |
fasta_for_db |
path to a fasta file to make the blast database |
database |
path to a blast database |
clean_pq |
(logical) If set to TRUE, empty samples and empty ASV are discarded after filtering. |
add_info_to_taxtable |
(logical, default TRUE) Does the blast information are added to the taxtable ? |
id_filter |
(default: 90) cut of in identity percent to keep result |
bit_score_filter |
(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_filter |
(default: 50) cut of in query cover (%) to keep result |
e_value_filter |
(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. |
... |
Others options for the |
A new phyloseq-class
object.
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