gff2cds

This function extracts CDS as DNAStringSet from GFF3 or GTF.

gff2cds(file, genome, format = "gff3", longest = TRUE, source = "NCBI")

Arguments

file

GFF or GTF file [mandatory]

genome

DNAStringSet [mandatory]

format

specify gff format either "gff3" or "gtf" [default: gff3]

longest

specify if longest isoform should be retained [default: TRUE]

source

source indicating either BAKTA, ENSEMBL, GEMOMA or NCBI [default: NCBI]

Value

DNAStringSet

See also

GFFFile-classXStringSet-class, GmakeTxDbFromGFF

Author

Kristian K Ullrich