importTranscripts: Import transcripts from GFF file

Description Usage Arguments Value Author(s) Examples

View source: R/misc.R

Description

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

Usage

1
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

1
2
3
4
5
## Not run: 
tx <- importTranscripts(file)

## End(Not run)
NULL

Bioconductor-mirror/SGSeq documentation built on June 23, 2017, 4:25 p.m.