importTranscripts: Import transcripts from GFF file

In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

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

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.