calculateCoverageProfileListFromTxdb {RCAS}R Documentation

calculateCoverageProfileListFromTxdb

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

calculateCoverageProfileListFromTxdb(queryRegions, txdb, 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

sampleN

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

Value

A list of data.frame objects 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 <- calculateCoverageProfileListFromTxdb(queryRegions = queryRegions,
                                                   txdb = txdb,
                                                sampleN = 1000)

[Package RCAS version 1.12.0 Index]