calculateCoverageProfile {RCAS} | R Documentation |
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
|
targetRegions |
GRanges object containing genomic coordinates of a target feature (e.g. exons) |
sampleN |
If set to a positive integer, |
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)