QCplots {ORFik} | R Documentation

## Correlation and coverage plots for ORFikQC

### Description

Correlation plots default to mRNA covering reads. Meta plots defaults to leader, cds, trailer.
Output will be stored in same folder as the libraries in df.
Correlation plots will be fpkm correlation and log2(fpkm + 1) correlation between samples.

### Usage

    QCplots(
      df,
      region = "mrna",
      stats_folder = QCfolder(df),
      plot.ext = ".pdf",
      complex.correlation.plots = TRUE,
      BPPARAM
    )

### Arguments

`df` | an ORFik `experiment`
`region` | a character (default: mrna), make raw count matrices of whole mrnas or one of (leaders, cds, trailers)
`stats_folder` | directory to save, default: `QCfolder(df)`
`plot.ext` | character, default: ".pdf". Alternatives: ".png" or ".jpg". Note that in pdf format the complex correlation plots become very slow to load!
`complex.correlation.plots` | logical, default TRUE. Add in addition to simple correlation plot two computationally heavy dots + correlation plots. Useful for deeper analysis, but takes longer time to run, especially on low-quality gpu computers. Set to FALSE to skip these.
`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.

### Details

Is part of `QCreport`

### Value

invisible(NULL) (objects stored to disc)

### See Also

Other QC report: `QCreport()`, `QCstats()`

[Package ORFik version 1.14.7 Index]