calculateCoverageProfile: calculateCoverageProfile

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

calculateCoverageProfile

Description

This function checks overlaps between input query regions and annotation features, and then calculates coverage profile along target regions.

Usage

calculateCoverageProfile(
  queryRegions,
  targetRegions,
  sampleN = 0,
  bin.num = 100,
  bin.op = "mean",
  strand.aware = TRUE
)

Arguments

queryRegions	GRanges object imported from a BED file using importBed function
targetRegions	GRanges object containing genomic coordinates of a target feature (e.g. exons)
sampleN	If set to a positive integer, targetRegions will be downsampled to sampleN regions
bin.num	Positive integer value (default: 100) to determine how many bins the targetRegions should be split into (See genomation::ScoreMatrixBin)
bin.op	The operation to apply for each bin: 'min', 'max', or 'mean' (default: mean). (See genomation::ScoreMatrixBin)
strand.aware	TRUE/FALSE (default: TRUE) The strands of target regions are considered.

Value

A ScoreMatrix object returned by genomation::ScoreMatrixBin function. Target regions are divided into 100 equal sized bins and coverage level is calculated in a strand-specific manner.

Examples

data(gff)
data(queryRegions)
txdbFeatures <- getTxdbFeaturesFromGRanges(gffData = gff)
df <- calculateCoverageProfile(queryRegions = queryRegions,
                              targetRegions = txdbFeatures$exons,
                                    sampleN = 1000)

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