getTransInfo: Get transcript information

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

Get transcript information

Description

Generate a data frame object that contains information about input genomic feature set and its mapping results over the transcriptome.

Usage

getTransInfo(A, txdb)

Arguments

A	Genomic feature set, which should be a GRanges object.
txdb	A TxDb object.

Value

A data.frame object containing the following components:

• index_trans: The label of transcripts.

• index_features: The label of genomic features.

• seqnames: The chr name.

• features_pos: The starting coordinate of each genomic feature.

• width_features: The width of each genomic feature.

• strand: The strand type of each genomic feature.

• trans_ID: The ids of the transcripts that each feature can be mapped to.

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
getTransInfo(A = m6A_sites_data[1:100], txdb)

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