View source: R/ortholog_funks.R
orthologsFromBLATpslTable | R Documentation |
Parses 'psl' default BLAT output formatted files to infer orthologs between species. Uses PERL regular expressions to identify which gene identifiers belongs to which species. Hence by using two such regular expressions orthologs between two species can be extracted, even though the BLAT output file contains similarity pairs from more than two species. Note that orthology is inferred based on reciprocal best search results.
orthologsFromBLATpslTable(blat.df, query.col = 10, target.col = 14,
matching.bases.col = 1, qSize.col = 11, tSize.col = 15,
spec.regexs = c("CAHR\\d+(\\.\\d)?",
"AT[0-9MC]G\\d+(\\.\\d)?"))
blat.df |
a data frame holding the output of BLAT in psl format. Se function readBlatPSLoutput(...) for more details |
query.col |
the number of the column in which to lookup the query sequence's name |
target.col |
the number of the column in which to lookup the target sequence's name |
matching.bases.col |
the number of the column in which to lookup the number of nucleotide bases matching between query and target |
qSize.col |
the number of the column in which to lookup the query sequence's size |
tSize.col |
the number of the column in which to lookup the target sequence's size |
spec.regexs |
a character vector containg two regular expressions matching gene identifiers from each of the two species orthologies are to be found for |
A data frame of two columns holding the gene identifiers of the orthologous gene pairs. Note, that for reasons of easing lookup inverse pairs are also contained.
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