summarizeQueryRegions: summarizeQueryRegions

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

summarizeQueryRegions

Description

This function counts number of query regions that overlap with different types of gene features.

Usage

summarizeQueryRegions(queryRegions, txdbFeatures)

Arguments

queryRegions	GRanges object imported from a BED file using importBed function
txdbFeatures	List of GRanges objects - outputs of getTxdbFeaturesFromGRanges and getTxdbFeatures functions

Value

A data frame with two columns where first column holds features and second column holds corresponding counts

Examples

data(gff)
data(queryRegions)
txdbFeatures <- getTxdbFeaturesFromGRanges(gffData = gff)
summary <- summarizeQueryRegions(queryRegions = queryRegions,
                                 txdbFeatures = txdbFeatures)

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