R/filter_homologs_core_set.R
filter_homologs_core_set.Rd
This function aims to retrieve a core set of best blast hits for each query sequence that is shared across all species. In other words, only query sequences
that generated blast hits in all species in the input blast_tbl
were retained.
by filtering a blast_tbl
using the following criteria.
A best hit is defined as (fulfilling all three critaria):
max(alig_length): only the hit having the longest alignment length is retained.
qcovhsp >= min_qcovhsp
: only hits that have a query coverage of at least min_qcovhsp
are retained.
max(bit_score): only the hit having the highest bit-score is retained.
filter_homologs_core_set(blast_tbl, min_qcovhsp = 50)
a BLAST table generated with detect_homologs_proteome_to_proteome
or detect_homologs_cds_to_cds
.
minimum query coverage of the hit in percent 0..100
that shall be retained. Default value is set to min_qcovhsp = 50
(= a best hit alignment must have at least 50 percent query coverage).