riboSeqR (version 1.6.0)

readingFrame: Analyses frame called ribosome footprint data within coding sequences and identifies likely frame-shift of different length ribosome footprint reads.

Description

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.

Usage

readingFrame(coordinates, riboDat, rC, lengths = 26:30)
plotFS(fS, lengths, legend.text = c("Frame 0", "Frame 1", "Frame 2"), ...)

Arguments

coordinates

Coordinates of transcripts. Need not be given if a riboCoding object is specified in `rC'.

riboDat

A riboData object containing the ribosome footprint data. Need not be given if a riboCoding object is specified in `rC'.

rC

A riboCoding object.

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.

Value

A matrix giving the number of aligned reads in each frame for each length, and the maximum likelihood frame.

See Also

frameCounting

Examples

#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)