calculateCoverageProfileFromTxdb {RCAS}R Documentation

calculateCoverageProfileFromTxdb

Description

This function overlaps the input query regions with a target list of annotation features and calculates the coverage profile along the target regions.

Usage

calculateCoverageProfileFromTxdb(queryRegions, txdb, type, sampleN = 0)

Arguments

queryRegions

GRanges object imported from a BED file using importBed function

txdb

A txdb object obtained by using GenomicFeatures::makeTxDb family of functions

type

A character string defining the type of gene feature for which a profile should be calculated. The options are: transcripts, exons, introns, promoters, fiveUTRs, threeUTRs, and cds.

sampleN

If set to a positive integer, the targetRegions will be downsampled to sampleN regions

Value

A data.frame object consisting of two columns: 1. coverage level 2. bins. The target regions are divided into 100 equal sized bins and coverage level is summarized in a strand-specific manner using the genomation::ScoreMatrixBin function.

Examples

data(gff)
data(queryRegions)
txdb <- GenomicFeatures::makeTxDbFromGRanges(gff)
df <- calculateCoverageProfileFromTxdb(queryRegions = queryRegions,
                                               type = 'exons',
                                               txdb = txdb,
                                            sampleN = 1000)

[Package RCAS version 1.6.0 Index]