calculateCoverageProfileList {RCAS} | R Documentation |
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.
calculateCoverageProfileList(queryRegions, targetRegionsList, sampleN = 0, bin.num = 100, bin.op = "mean", strand.aware = TRUE)
queryRegions |
GRanges object imported from a BED file using
|
targetRegionsList |
A list of GRanges objects containing genomic coordinates of target features (e.g. transcripts, exons, introns) |
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 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
)
data(gff) data(queryRegions) txdbFeatures <- getTxdbFeaturesFromGRanges(gffData = gff) dfList <- calculateCoverageProfileList(queryRegions = queryRegions, targetRegionsList = txdbFeatures, sampleN = 1000)