transcriptWindow1 {ORFik} | R Documentation

## Meta coverage over all transcripts

### Description

Given as single window

### Usage

    transcriptWindow1(
      df,
      outdir = NULL,
      scores = c("sum", "zscore"),
      colors = rep("skyblue4", nrow(df)),
      title = "Coverage metaplot",
      windowSize = 100,
      returnPlot = is.null(outdir),
      dfr = NULL,
      idName = "",
      format = ".png",
      type = "ofst",
      BPPARAM = bpparam()
    )

### Arguments

`df` | an ORFik `experiment`
`outdir` | directory to save to (default: NULL, no saving)
`scores` | scoring function (default: c("sum", "zscore")), see ?coverageScorings for possible scores.
`colors` | Which colors to use, default (skyblue4)
`title` | title of ggplot
`windowSize` | size of binned windows, default: 100
`returnPlot` | return plot from function, default is.null(outdir), so TRUE if outdir is not defined.
`dfr` | an ORFik `experiment` of RNA-seq to normalize against. Will add RNA normalized to plot name if this is done.
`idName` | A character ID to add to saved name of plot, if you make several plots in the same folder, and same experiment, like splitting transcripts in two groups like targets / nontargets etc. (default: "")
`format` | default (".png"), do ".pdf" if you want as pdf
`type` | a character(default: "bedoc"), load files in experiment or some precomputed variant, either "bedo", "bedoc", "pshifted" or default. These are made with ORFik:::simpleLibs(), shiftFootprintsByExperiment().. Will load default if bedoc is not found
`BPPARAM` | how many cores/threads to use? default: bpparam()

### Value

NULL, or ggplot object if returnPlot is TRUE

### See Also

Other experiment plots: `transcriptWindowPer()`, `transcriptWindow()`

[Package ORFik version 1.8.6 Index]