findCDS {riboSeqR} | R Documentation

## Parses a transcriptome file looking for start/stop codons in frame.

### Description

Looks in the fastaFile for defined start and stop codons in frame with one another. Reports the discovered coordinates as a GRanges object with a ‘frame’ value.

### Usage

    findCDS(fastaFile, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))

### Arguments

`fastaFile` | Fasta file of transcriptome sequences.
`startCodon` | Vector of possible start codons. Defaults to "ATG".
`stopCodon` | Vector of possible stop codons. Defaults to c("TAG", "TAA", "TGA").

### Value

A GRanges object.

### Author(s)

Thomas J. Hardcastle

### Examples

    datadir <- system.file("extdata", package = "riboSeqR")
    chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
    fastaCDS <- findCDS(fastaFile = chlamyFasta,
                        startCodon = c("ATG"),
                        stopCodon = c("TAG", "TAA", "TGA"))

[Package riboSeqR version 1.18.0 Index]