importTranscripts {SGSeq} | R Documentation

## Import transcripts from GFF file

### Description

Import GFF file and generate a `GRangesList` of transcripts suitable as input for functions `convertToTxFeatures` or `predictVariantEffects`.

### Usage

    importTranscripts(file, tag_tx = "transcript_id", tag_gene = "gene_id")

### Arguments

`file` | Character string specifying input GFF file
`tag_tx` | GFF attribute tag for transcript identifier
`tag_gene` | GFF attribute tag for gene identifier

### Value

`GRangesList` of exons grouped by transcipts with metadata columns txName, geneName, cdsStart, cdsEnd.

### Author(s)

Leonard Goldstein

### Examples

    ## Not run:
    tx <- importTranscripts(file)

    ## End(Not run)
    NULL

[Package SGSeq version 1.21.9 Index]