breakTranscriptsOnGenes {groHMM} | R Documentation

## breakTranscriptsOnGenes Breaks transcripts on genes

### Description

Breaks transcripts when they are overlapped with multiple well annotated genes.

### Usage

    breakTranscriptsOnGenes(tx, annox, strand = "+", geneSize = 5000,
      threshold = 0.8, gap = 5, plot = FALSE)

### Arguments

`tx` | GRanges of transcripts.
`annox` | GRanges of non-overlapping annotations for reference.
`strand` | Takes "+" or "-" Default: "+"
`geneSize` | Numeric. Minimum gene size in annox to be used as reference. Default: 5000
`threshold` | Numeric. Ratio of overlapped region relative to a gene width. Transcripts only greater than this threshold are subjected to be broken. Default: 0.8
`gap` | Numeric. Gap (bp) between broken transcripts. Default: 5
`plot` | Logical. If set to TRUE, show each step in a plot. Default: FALSE

### Value

Returns GRanges object of broken transcripts.

### Author(s)

Minho Chae and Charles G. Danko

### Examples

    tx <- GRanges("chr7", IRanges(1000, 30000), strand="+")
    annox <- GRanges("chr7", IRanges(start=c(1000, 20000),
                 width=c(10000,10000)), strand="+")
    bPlus <- breakTranscriptsOnGenes(tx, annox, strand="+")

[Package groHMM version 1.18.0 Index]