convertToTxFeatures: Convert to TxFeatures object

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

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.

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). For import from GFF format, use function importTranscripts.

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).

Value

TxFeatures object

Author(s)

Leonard Goldstein

Examples

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

SGSeq documentation built on Nov. 8, 2020, 8:31 p.m.