overlapCountsTx: Evaluation function

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

Evaluation function

Description

This function receives two region sets and returns the number of their overlaps.

Usage

overlapCountsTx(A, B, count_once = TRUE, over_trans = TRUE, ...)

Arguments

A	Region set 1. A GRangesList object.
B	Region set 2. A GRangesList object.
count_once	Whether the overlap of multiple B regions with a single A region should be counted once or multiple times.
over_trans	Whether the overlapping is counted over the transcriptome or over the genome.
...	Any additional parameters needed.

Value

A numeric object.

See Also

overlapCountsTx

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
trans.ids <- c("170", "782", "974", "1364", "1387")
exons.tx0 <- exonsBy(txdb)
regions.A <- exons.tx0[trans.ids]
A <- randomizeTransByOrder(regions.A, random_length = 200)
B <- randomizeTransByOrder(regions.A, random_length = 200)

overlapCountsTx(A, B)

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