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",
      weight = "score",
      drop.zero.dt = FALSE,
      BPPARAM = bpparam()
    )

### 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 (columns). All genes with region smaller than this size are filter out for metacoverage.
`fraction` | a character (1), info on reads (which read length, or which type (RNA seq)) (row names)
`weight` | (default: 'score'), if defined a character name of valid meta column in subject. GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times. ORFik ofst, bedoc and .bedo files contains a score column like this. As do CAGEr CAGE files and many other package formats. You can also assign a score column manually.
`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

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 1.12.13 Index]