frameCounting {riboSeqR} | R Documentation |
Ribosome footprint sequencing reads aligning within coding sequence regions may align in the same frame (relative to start codon) as the coding sequence, or frame shifted by 1 or 2 frames. This function calls the number of aligning reads within the coding sequence, split by frame and footprint size.
frameCounting(riboDat, cds, lengths = 25:30, offset5p = 0, offset3p = 0)
riboDat |
A |
cds |
A |
lengths |
Lengths of ribosome footprints to be included in the |
offset5p |
An offset to the 5' end of the coding sequence coordinates to include ribosome footprints some distance upstream of coding start. |
offset3p |
An offset to the 3' end of the coding sequence coordinates to exclude reads too close to coding stop. |
A riboCoding
object.
Thomas J. Hardcastle
riboData
#ribosomal footprint data datadir <- system.file("extdata", package = "riboSeqR") ribofiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "") rnafiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "") riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT", "M", "M")) # CDS coordinates chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "") fastaCDS <- findCDS(fastaFile = chlamyFasta, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA")) # frame calling fCs <- frameCounting(riboDat, fastaCDS)