getTargetedGenesTable: getTargetedGenesTable

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

getTargetedGenesTable

Description

This function provides a list of genes which are targeted by query regions and their corresponding numbers from an input BED file. Then, the hits are categorized by the gene features such as promoters, introns, exons, 5'/3' UTRs and whole transcripts.

Usage

getTargetedGenesTable(queryRegions, txdbFeatures)

Arguments

queryRegions	GRanges object containing coordinates of input query regions imported by the importBed function
txdbFeatures	A list of GRanges objects where each GRanges object corresponds to the genomic coordinates of gene features such as promoters, introns, exons, 5'/3' UTRs and whole transcripts. This list of GRanges objects are obtained by the function getTxdbFeaturesFromGRanges or getTxdbFeatures.

Value

A data.frame object where rows correspond to genes and columns correspond to gene features

Examples

data(gff)
data(queryRegions)
txdbFeatures <- getTxdbFeaturesFromGRanges(gffData = gff)
featuresTable <- getTargetedGenesTable(queryRegions = queryRegions,
                                       txdbFeatures = txdbFeatures)

#or
## Not run: 
txdb <- GenomicFeatures::makeTxDbFromGRanges(gff)
txdbFeatures <- getTxdbFeatures(txdb)
featuresTable <- getTargetedGenesTable(queryRegions = queryRegions,
                                       txdbFeatures = txdbFeatures)
                                       
## End(Not run)

BIMSBbioinfo/RCAS documentation built on Feb. 7, 2024, 4:38 p.m.