overlapCountsTxIA: 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 receives a feature set (with isoform ambiguity) and a transcriptome region set (without isoform ambiguity), and returns a weighted number of overlaps between them.

Usage

overlapCountsTxIA(A, B, ...)

Arguments

A	A feature set, which should be GRanges.
B	A region set, which should be GRangesList.
...	Any additional parameters needed.

Value

A numeric object.

See Also

overlapWidthTx, distanceTx, overlapCountsTx

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]

trans.info <- getTransInfo(RS1, txdb)
trans.ids <- trans.info[, "trans_ID"]

RS2 <- getStopCodon(trans.ids, txdb = txdb)

# Evaluation step.
orig.ev <- overlapCountsTxIA(RS1, RS2)

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