TxFeatures: Transcript features

Description Usage Arguments Details Value Author(s) Examples

View source: R/classes.R

Description

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

Usage

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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

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

ldg21/SGSeq documentation built on May 7, 2019, 9:37 a.m.