calculateCoverageProfileListFromTxdb {RCAS} | R Documentation |
This function overlaps the input query regions with a target list of annotation features and calculates the coverage profile along the target regions.
calculateCoverageProfileListFromTxdb(queryRegions, txdb, sampleN = 0)
queryRegions |
GRanges object imported from a BED file using
|
txdb |
A txdb object obtained by using |
sampleN |
If set to a positive integer, |
A list of data.frame objects consisting of two columns: 1. coverage
level 2. bins. The target regions are divided into 100 equal sized bins and
coverage level is summarized in a strand-specific manner using the
genomation::ScoreMatrixBin
function.
data(gff) data(queryRegions) txdb <- GenomicFeatures::makeTxDbFromGRanges(gff) df <- calculateCoverageProfileListFromTxdb(queryRegions = queryRegions, txdb = txdb, sampleN = 1000)