ExtractGenes: Extract Predicted Genes from a Genome

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

Description

Extracts predicted genes from the genome used for prediction.

Usage

ExtractGenes(x,
             myDNAStringSet,
             type = "DNAStringSet",
             ...)

Arguments

x	An object of class Genes.
myDNAStringSet	The DNAStringSet object used in generating x.
type	The class of sequences to return. This should be (an unambiguous abbreviation of) one of "AAStringSet", "DNAStringSet" (the default), or "RNAStringSet".
...	Other parameters passed directly to translate.

Details

Extracts a set of gene predictions as either DNA, mRNA, or proteins.

Value

An "AAStringSet", "DNAStringSet", or "RNAStringSet" determined by type.

Author(s)

Erik Wright [e-mail]

See Also

FindGenes, Genes-class, WriteGenes

Examples

# import a test genome
fas <- system.file("extdata",
	"Chlamydia_trachomatis_NC_000117.fas.gz",
	package="DECIPHER")
genome <- readDNAStringSet(fas)

x <- FindGenes(genome)
genes <- ExtractGenes(x, genome)
proteins <- ExtractGenes(x, genome, type="AAStringSet")

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.