ExtractGenes {DECIPHER} | R Documentation

## Extract Predicted Genes from a Genome

### 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 eswright@pitt.edu

### 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")

[Package DECIPHER version 2.22.0 Index]