SGSeq (version 1.4.0)

importTranscripts: 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

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

Examples

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