calculateCoverageProfileFromTxdb {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.
calculateCoverageProfileFromTxdb(queryRegions, txdb, type, sampleN = 0)
queryRegions |
GRanges object imported from a BED file using
|
txdb |
A txdb object obtained by using |
type |
A character string defining the type of gene feature for which a profile should be calculated. The options are: transcripts, exons, introns, promoters, fiveUTRs, threeUTRs, and cds. |
sampleN |
If set to a positive integer, the targetRegions will be
downsampled to |
A data.frame object 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 <- calculateCoverageProfileFromTxdb(queryRegions = queryRegions, type = 'exons', txdb = txdb, sampleN = 1000)