rnaCounts {riboSeqR} | R Documentation

## Extracts mRNA counts from a riboDat object for a set of coding sequence coordinates.

### Description

Takes mRNA count data from riboDat object, maps them to coding sequences specified in GRanges object, and counts the total number of hits. This is a crude approach intended to quickly produce comparable data to ribosome footprint counts. More sophisticated alternatives, addressing coverage variation, isoforms, multireads &c. have been widely described in the literature on mRNA-seq analyses.

### Usage

    rnaCounts(riboDat, CDS)

### Arguments

`riboDat` | A `riboData` object containing the RNA-seq alignments.
`CDS` | A `GRanges` object defining the coordinates of the coding sequences for which to acquire counts.

### Details

The count data thus acquired can be compared to counts of ribosomal footprint data through a beta-binomial analysis (see vignette) to discover differential translation.

### Value

A matrix containing count data for the RNA-seq libraries.

### Author(s)

Thomas J. Hardcastle

### See Also

`sliceCounts`

### 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)

    # analysis of frame shift for 27 and 28-mers.
    fS <- readingFrame(rC = fCs, lengths = 27:28)

    # filter coding sequences. 27-mers are principally in the 1-frame,
    # 28-mers are principally in the 0-frame relative to coding start (see
    # readingFrame function).

    ffCs <- filterHits(fCs, lengths = c(27, 28), frames = list(1, 0),
                       hitMean = 50, unqhitMean = 10, fS = fS)

    # Extract counts of RNA hits from riboCount data.
    rnaCounts <- rnaCounts(riboDat, ffCs@CDS)

[Package riboSeqR version 1.16.0 Index]