SGFeatures: Splice graph features

In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

Description

Creates an instance of S4 class SGFeatures for storing splice graph features.

Usage

SGFeatures(x, type = mcols(x)$type, splice5p = mcols(x)$splice5p,
  splice3p = mcols(x)$splice3p, featureID = mcols(x)$featureID,
  geneID = mcols(x)$geneID, txName = mcols(x)$txName,
  geneName = mcols(x)$geneName)

Arguments

x	GRanges with known strand (“+”, “-”)
type	Character vector or factor taking value J, E, D, or A
splice5p	Logical vector indicating a mandatory splice at the 5' end of an exon bin (determining whether reads extending across the 5' boundary must be spliced to be considered compatible)
splice3p	Logical vector indicating a mandatory splice at the 3' end of an exon bin (determining whether reads extending across the 3' boundary must be spliced to be considered compatible)
featureID	Integer vector of feature IDs
geneID	Integer vector of gene IDs
txName	CharacterList of transcript names or NULL
geneName	CharacterList of gene names or NULL

Details

SGFeatures extends GRanges with column slot type specifying feature type. type is a factor with levels J (splice junction), E (exon bin), D (splice donor), A (splice acceptor).

splice5p and splice3p are logical vectors indicating mandatory splices at the 5' and 3' end of an exon bin, respectively. These are used to determine whether reads extending across the 5' and 3' boundaries of an exon bin must be spliced at the boundary to be considered compatible with the exon bin.

featureID and geneID are integer vectors representing unique identifiers for features and genes (connected components in the splice graph).

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

Value

SGFeatures object

Author(s)

Leonard Goldstein

Examples

sgf <- SGFeatures()

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.