randomizeFeaturesTx: 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.

Usage

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

Arguments

RS	The feature to be 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	The number of iterations.
...	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, randomizeFeaturesTxIA, randomizeTx

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
trans.ids <- c("170", "782", "974", "1364", "1387")
RS1 <- randomizeTx(txdb, trans.ids, random_num = 100, random_length = 100)
RS <- randomizeFeaturesTx(RS1, txdb, N = 1)

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