summarizeQueryRegions: summarizeQueryRegions
In RCAS: RNA Centric Annotation System

Description Usage Arguments Value Examples

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

1	summarizeQueryRegions(queryRegions, txdbFeatures)

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

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

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