orfFrameDistributions {ORFik} | R Documentation

## Find shifted Ribo-seq frame distributions

### Description

Per library: get coverage over CDS per frame per readlength Return as data.datable with information and best frame found. Can be used to automize re-shifting of read lengths (find read lengths where frame 0 is not the best frame over the entire cds)

### Usage

    orfFrameDistributions(
      df,
      type = "pshifted",
      weight = "score",
      BPPARAM = BiocParallel::bpparam()
    )

### Arguments

`df` | an ORFik `experiment`
`type` | type of library loaded, default pshifted, warning if not pshifted might crash if too many read lengths!
`weight` | which column in reads describe duplicates, default "score".
`BPPARAM` | how many cores/threads to use? default: bpparam(). To see number of threads used, do `bpparam()$workers`. You can also add a time remaining bar, for a more detailed pipeline.

### Value

data.table with columns: fraction (library) frame (0, 1, 2) score (coverage) length (read length) percent (coverage percentage of library) percent_length (coverage percentage of library and length) best_frame (TRUE/FALSE, is this the best frame per length)

### Examples

    df <- ORFik.template.experiment()[3,]
    dt <- orfFrameDistributions(df, BPPARAM = BiocParallel::SerialParam())
    ## Check that frame 0 is best frame for all
    all(dt[frame == 0,]$best_frame)

[Package ORFik version 1.14.7 Index]