SGSeq (version 1.6.5)

SGFeatures: Splice graph features

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

Value

SGFeatures object

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.

Examples

sgf <- SGFeatures()