Description Usage Arguments Value See Also Examples
Given a tbl of blast output format 7 hits can be filtered by evalue
, bit_score
, query_cov
, identity
and query_length
1 2 3 4 5 6 7 8 |
blast_tbl |
an object of class tbl from blast output format 7. It must contains below columns.
Column names can be assigned using the function |
evalue |
a numeric value; default NULL. Only hits having evalue <= than given will be retained. |
bit_score |
a numeric value; default NULL. Only hits having bit_score >= than given will be retained. |
query_cov |
a numeric value between 0 and 100 ; default NULL. Only hits having query_cov >= than given will be retained. query_cov will be calculated from the column |
identity |
a numeric value between 0 and 100;default NULL. Only hits having identity >= than given will be retained. |
query_length |
a numeric value indicating length of query sequence. |
a tbl of filtered blast hits.
get_blast_outformat_7_colnames
1 2 3 4 5 6 7 8 9 10 11 | ## Not run:
f <- system.file("extdata","blast_output_01.txt" ,package = "phyloR")
d <- readr::read_delim(f, delim ="\t" , col_names = F , comment = "#")
colnames(d) <- phyloR::get_blast_outformat_7_colnames()
filtered <- filter_blast_hits(d ,
query_cov = 90 ,
identity = 40,
query_length = 249,
evalue = 1e-6)
## End(Not run)
|
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