getPermSpaceByFeatures: Get permutation space for features

In yue-wang-biomath/RgnTX: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

Get permutation space for features

Description

This function returns a default permutation space for features with isoform ambiguity. The default permutation space of a feature is the aggregate of the multiple transcripts it may overlap with. It requires the input feature to be GRanges format.

Usage

getPermSpaceByFeatures(features, txdb, type = "mature")

Arguments

features	A GRanges object.
txdb	A TxDb object.
type	A character object. Default is "mature". It accepts options "mature", "full", "fiveUTR", "CDS" or "threeUTR", with which one can get corresponding types of regions over transcriptome.

Value

A list object, which contains two elements.

• perm.space: A GRangesList object that includes all the transcripts input features may overlap with.

• index: It contains a series of numbers indicating which feature these transcripts are respectively associated with.

See Also

getPermSpaceByTxID, getPermSpaceByType

yue-wang-biomath/RgnTX documentation built on Aug. 24, 2023, 1:12 p.m.