SGSeq (version 1.4.0)

convertToTxFeatures: Convert to TxFeatures object

Description

Convert a TxDb object or a GRangesList of exons grouped by transcripts to a TxFeatures object.

Usage

convertToTxFeatures(x)

Arguments

x

TxDb object or GRangesList of exons grouped by transcript. For import from GFF format, use function importTranscripts.

Value

A TxFeatures object

Details

If x is a GRangesList, transcript names and gene names can be specified as character vectors in metadata columns txName and geneName, respectively. If missing, transcript names are based on names(x).

In the returned TxFeatures object, column type takes values “J” (splice junction), “I” (internal exon), “F” (5'/first exon), “L” (3'/last exon) or “U” (unspliced).

Examples

gr <- GRanges(c(1, 1), IRanges(c(1, 201), c(100, 300)), c("+", "+"))
grl <- split(gr, 1)
txf <- convertToTxFeatures(grl)