findCDS {riboSeqR} | R Documentation |
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.
findCDS(fastaFile, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))
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"). |
A GRanges object.
Thomas J. Hardcastle
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"))