exportToGtf {eisaR} | R Documentation

## Export GRangesList to GTF

### Description

Export the features in a GRangesList generated by `getFeatureRanges` to a GTF file. The function will represent each row of each of the entries as an "exon", each individual entry as a "transcript", and aggregate all features belonging to the same gene as a "gene" entry in the GTF file.

### Usage

    exportToGtf(grl, filepath)

### Arguments

`grl` | `GRangesList` object, typically generated by `getFeatureRanges`
`filepath` | Path to output GTF file

### Value

Does not return anything, generates a GTF file

### Author(s)

Charlotte Soneson

### Examples

      ## Get feature ranges
      grl <- getFeatureRanges(
        gtf = system.file("extdata/small_example.gtf", package = "eisaR"),
        featureType = c("spliced", "intron"),
        intronType = "separate",
        flankLength = 5L,
        joinOverlappingIntrons = FALSE,
        verbose = TRUE
      )

      ## Export GTF
      exportToGtf(grl = grl, filepath = file.path(tempdir(), "exported.gtf"))

[Package eisaR version 1.2.0 Index]