frameCounting {riboSeqR} | R Documentation

## Counts aligned reads within coding sequence regions by frame and footprint size, splitting by frame and footprint size.

### Description

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.

### Usage

    frameCounting(riboDat, cds, lengths = 25:30, offset5p = 0, offset3p = 0)

### Arguments

`riboDat` | A `riboData` object containing the ribosome footprints to be counted.
`cds` | A `GenomicRanges` object containing the coordinates of the coding sequences.
`lengths` | Lengths of ribosome footprints to be included in the `riboData` object.
`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.

### Value

A `riboCoding` object.

### Author(s)

Thomas J. Hardcastle

### See Also

`riboData`

### 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
    fCs <- frameCounting(riboDat, fastaCDS)

[Package riboSeqR version 1.26.0 Index]