calculateCoverageProfileList {RCAS} | R Documentation

## 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)

[Package RCAS version 1.14.0 Index]