TxFeatures: Transcript features

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

Description

Creates an instance of S4 class TxFeatures for storing transcript features.

Usage

TxFeatures(x, type = mcols(x)$type, txName = mcols(x)$txName,
  geneName = mcols(x)$geneName)

Arguments

x	GRanges with known strand (“+”, “-”)
type	Character vector or factor, taking value J, I, F, L, or U
txName	CharacterList of transcript names or NULL
geneName	CharacterList of gene names or NULL

Details

TxFeatures extends GRanges with column slot type specifying feature type. type is a factor with levels J (splice junction), I (internal exon), F (5' terminal exon), L (3' terminal exon), U (unspliced transcript).

txName and geneName are CharacterLists storing transcript and gene annotation, respectively.

Value

TxFeatures object

Author(s)

Leonard Goldstein

Examples

gr <- GRanges(1, IRanges(101, 200), "+")
txf <- TxFeatures(gr, type = "J")

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