readingFrame {riboSeqR} | R Documentation |
Ribosome footprint data data can be used to identify the frame-shift relative to start codon of the different n-mers. For each readlength specified, the sum of alignments in the different frames is shown, together with the maximum likelihood frame.
readingFrame(rC, lengths = 26:30) plotFS(fS, lengths, legend.text = c("Frame 0", "Frame 1", "Frame 2"), ...)
rC |
A riboCoding object, produced by the |
lengths |
Lengths of reads to be analysed for frame-shift, or to be plotted. May be omitted in plotting, in which case all lengths will be plotted. |
fS |
The output of the readingFrame function, to be plotted. |
legend.text |
Text for legend. |
... |
Additional arguments to be passed to barplot function. |
A matrix giving the number of aligned reads in each frame for each length, and the maximum likelihood frame.
Thomas J. Hardcastle
#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 rCs <- frameCounting(riboDat, fastaCDS) # analysis of frame shift for 27 and 28-mers. fS <- readingFrame(rC = rCs, lengths = 27:28) plotFS(fS)