randomizeFeaturesTxIA: Randomize features into transcriptome

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

Randomize features into transcriptome

Description

Randomize features into transcriptome, especially for the features that have isoform ambiguity.

Usage

randomizeFeaturesTxIA(RS, txdb, type = "mature", N = 1, ...)

Arguments

RS	The feature being randomized. It should be a GRanges or GRangesList 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 transcriptome regions.
N	Randomization times.
...	Any additional parameters needed.

Value

A GRangesList object. The name of each element is the id of the transcript where the corresponding range is located.

See Also

randomizeTransByOrder, randomizeFeaturesTx, randomizeTx

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
file <- system.file(package="RgnTX", "extdata/m6A_sites_data.rds")
m6A_sites_data <- readRDS(file)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
RS1 <- m6A_sites_data[1:100]
RS <- randomizeFeaturesTxIA(RS1, txdb, N = 1)

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