getTargetedGenesTable {RCAS} | R Documentation

## 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)

[Package RCAS version 1.12.0 Index]