Description Usage Arguments Value Author(s) See Also Examples
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.
1 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | #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)
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