SGSeq (version 1.0.6)

SGFeatures: Constructor function for S4 class SGFeatures

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 values in J, E, D, A

splice5p

Logical vector indicating whether reads extending across the 5' boundary of an exon bin must be spliced at the boundary

splice3p

Logical vector indicating whether reads extending across the 3' boundary of an exon bin must be spliced at the boundary

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

An SGFeatures object

Details

SGFeatures extend 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 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()