distanceTx: Evaluation function

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

Evaluation function

Description

Evaluation function. This function calculates the mean of the distance from each region of set RS1 to the closest region in RS2.

Usage

distanceTx(A, B, beta = 0.2, ...)

Arguments

A	Region set 1. A Granges or GRangesList object.
B	Region set 2. A Granges or GRangesList object.
beta	It is a user-defined argument that can filter out the corresponding percent of largest distance values. Default value is 0.2.
...	Any additional parameters needed.

Value

A numeric object.

See Also

overlapWidthTx, overlapCountsTx

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
trans.ids <- c("170", "782", "974", "1364", "1387")
A <- randomizeTx(
    txdb, trans.ids,
    random_num = 20,
    random_length = 100
)
B <- randomizeTx(
    txdb, trans.ids,
    random_num = 20,
    random_length = 100
)
distanceTx(A, B, beta = 0.2)

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