windowPerTranscript {ORFik} | R Documentation

## Get a binned coverage window per transcript

### Description

Per transcript (or other regions), bin them all to windowSize (default 100), and make a data.table, rows are positions, useful for plotting with ORFik and ggplot2.

### Usage

    windowPerTranscript(
      txdb,
      reads,
      splitIn3 = TRUE,
      windowSize = 100,
      fraction = "1"
    )

### Arguments

`txdb` | a TxDb object or a path to gtf/gff/db file.
`reads` | GRanges or GAlignment of reads
`splitIn3` | a logical(TRUE), split window in 3 (leader, cds, trailer)
`windowSize` | an integer (100), size of windows
`fraction` | a character (1), info on reads (which read length, or which type (RNA seq))

### Details

NOTE: All ranges with smaller width than windowSize, will of course be removed. What is the 100th position on a 1 width object ?

### Value

a data.table with columns position, score

[Package ORFik version 1.6.9 Index]