splitIn3Tx {ORFik} | R Documentation

## Create binned coverage of transcripts, split into the 3 parts.

### Description

The 3 parts of transcripts are the leaders, the cds' and trailers. Per transcript part, bin them all to windowSize (default 100), and make a data.table, rows are positions, useful for plotting with ORFik and ggplot2.

### Usage

    splitIn3Tx(
      leaders,
      cds,
      trailers,
      reads,
      windowSize = 100,
      fraction = "1",
      weight = "score",
      is.sorted = FALSE,
      drop.zero.dt = FALSE,
      BPPARAM = BiocParallel::SerialParam()
    )

### Arguments

`leaders` | a `GRangesList` of leaders (5' UTRs)
`cds` | a `GRangesList` of coding sequences
`trailers` | a `GRangesList` of trailers (3' UTRs)
`reads` | GRanges or GAlignment of reads
`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.
`is.sorted` | logical (FALSE), is grl sorted. That is + strand groups in increasing ranges (1,2,3), and - strand groups in decreasing ranges (3,2,1)
`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()

### Value

a data.table with columns position, score

[Package ORFik version 1.12.13 Index]