readingFrame {riboSeqR} | R Documentation

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

### Arguments

`rC` | A riboCoding object, produced by the `frameCounting` function.
`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.

### Author(s)

Thomas J. Hardcastle

### 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)

[Package riboSeqR version 1.20.0 Index]