calculateCoverageProfileList: calculateCoverageProfileList

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

calculateCoverageProfileList

Description

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

Usage

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

Arguments

queryRegions	GRanges object imported from a BED file using importBed function
targetRegionsList	A list of GRanges objects containing genomic coordinates of target features (e.g. transcripts, exons, introns)
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 data.frame consisting of four columns: 1. bins level 2. meanCoverage 3. standardError 4. feature Target regions are divided into 100 equal sized bins and coverage level is summarized in a strand-specific manner using the genomation::ScoreMatrixBin function. For each bin, mean coverage score and the standard error of the mean coverage score is calculated (plotrix::std.error)

Examples

data(gff)
data(queryRegions)
txdbFeatures <- getTxdbFeaturesFromGRanges(gffData = gff)
dfList <- calculateCoverageProfileList(queryRegions = queryRegions,
                              targetRegionsList = txdbFeatures,
                                    sampleN = 1000)

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