utilsScoreOverlaps: Utility: Counting overlaps taking into account scores

In CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Description

Similar to countOverlaps, but takes the score column into account.

Usage

utilsScoreOverlaps(query, subject, ...)

Arguments

query	same as findOverlaps/countOverlaps
subject	same as findOverlaps/countOverlaps
...	additional arguments passed to findOverlaps

Value

vector of number of overlaps weigthed by score column.

See Also

https://support.bioconductor.org/p/87736/#87758

Other Utility functions: utilsAggregateRows(), utilsDeStrand(), utilsSimplifyTxDb()

Examples

gr1 <- GRanges(seqnames="chr1",
               ranges=IRanges(start = c(4, 9, 10, 30),
                              end = c(4, 15, 20, 31)),
               strand="+")
gr2 <- GRanges(seqnames="chr1",
               ranges=IRanges(start = c(1, 4, 15, 25),
                              end = c(2, 4, 20, 26)),
               strand=c("+"),
               score=c(10, 20, 15, 5))
countOverlaps(gr1, gr2)
utilsScoreOverlaps(gr1, gr2)

CAGEfightR documentation built on Nov. 8, 2020, 5:42 p.m.