transcriptWindowPer {ORFik} | R Documentation

## Helper function for transcriptWindow

### Description

Make 100 bases size meta window for one library in experiment

### Usage

    transcriptWindowPer(
      leaders,
      cds,
      trailers,
      df,
      outdir = NULL,
      scores = c("sum", "zscore"),
      reads,
      returnCoverage = FALSE,
      windowSize = 100,
      drop.zero.dt = TRUE,
      BPPARAM = bpparam()
    )

### Arguments

`leaders` | a `GRangesList` of leaders (5' UTRs)
`cds` | a `GRangesList` of coding sequences
`trailers` | a `GRangesList` of trailers (3' UTRs)
`df` | an ORFik `experiment`
`outdir` | directory to save to (default: NULL, no saving)
`scores` | scoring function (default: c("sum", "transcriptNormalized")), see ?coverageScorings for possible scores.
`reads` | a GRanges / GAligment object of reads, can also be a list of those.
`returnCoverage` | return data.table with coverage (default: FALSE)
`windowSize` | size of binned windows, default: 100
`drop.zero.dt` | logical FALSE, if TRUE and as.data.table is TRUE, remove all 0 count positions. This greatly speeds up and most importantly, greatly reduces memory usage. Will not change any plots, unless 0 positions are used in some sense. (mean, median, zscore coverage will only scale differently)
`BPPARAM` | how many cores/threads to use? default: bpparam()

### Details

Gives you binned meta coverage plots, either saved seperatly or all in one.

### Value

NULL, or ggplot object if returnPlot is TRUE

### See Also

Other experiment plots: `transcriptWindow1()`, `transcriptWindow()`

[Package ORFik version 1.12.13 Index]