calculateCoverageProfileList: calculateCoverageProfileList

Description Usage Arguments Value Examples

View source: R/report_functions.R

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

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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

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

RCAS documentation built on Nov. 1, 2018, 2:54 a.m.