combineTranscripts {groHMM} | R Documentation

## combineTranscripts Combines transnscipts.

### Description

Combines transcripts that are within the same gene annotation, combining smaller transcripts for genes with low regulation into a single transcript representing the gene.

### Usage

    combineTranscripts(tx, annox, geneSize = 1000, threshold = 0.8,
      plot = FALSE)

### Arguments

`tx` | GRanges of transcripts.
`annox` | GRanges of non-overlapping annotations for reference.
`geneSize` | Numeric. Minimum gene size in annotations to be used as reference. Default: 1000
`threshold` | Numeric. Ratio of overlapped region relative to transcript width. Transcripts only greater than this threshold are subjected to be combined. Default: 0.8
`plot` | Logical. If set to TRUE, show easch step in a plot. Default: FALSE

### Value

Returns GRanges object of combined transcripts.

### Author(s)

Minho Chae and Charles G. Danko

### Examples

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

[Package groHMM version 1.20.0 Index]