make_blastp_map: Map intervals for protein blast

In arendsee/synder: Use Synteny to Filter Genomic Search

Description

Returns info on the focal and target intervals where 1) there is a significant protein BLAST hit to the proteins encoded by the focal and target features and 2) the hit overlaps a search interval on the target side. The columns fseqid and si_fseqid hold the protein encoding focal feature and the focal interval used in the synder search, respectively. These two will not always be the same.

Usage

make_blastp_map(blastp_file, fgff, tgff, srcres, fmap = NULL,
  tmap = NULL, ffromAttr = identity, tfromAttr = identity)

Arguments

blastp_file	filename: with columns qseqid, sseqid, qlen, slen, length, evalue, ppos
fgff	GFF: focal species
tgff	GFF: target species
srcres	SearchResult object (from .tidy_searchResult)
fmap	data.frame: a map from blastp qseqid (a protein ID) to the seqid in the SearchResult (probably a gene ID for an interval)
tmap	data.frame: like fmap but for the target proteins
ffromAttr	function (optional) extract IDs attr column in focal GFF
tfromAttr	function (optional) extract IDs attr column in target GFF

Value

list containing the blast results filtered through synder and the raw blast results

arendsee/synder documentation built on May 10, 2019, 1:26 p.m.