calculateCoverageProfile: calculateCoverageProfile
In RCAS: RNA Centric Annotation System

Description Usage Arguments Value Examples

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

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

`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.

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.

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