riboSeqR (version 1.6.0)

findCDS: 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.

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"))