countSignal: Count the Sites Carrying an Arbitrary Signal Inside Genomic...
In genomaths/MethylIT.utils: MethylIT utility

countSignal

R Documentation

Count the Sites Carrying an Arbitrary Signal Inside Genomic Regions

Description

A simple function to count the number of sites carrying an arbitrary signal, which are inside given genomic regions.

Usage

countSignal(signal, gr, maxDist = NULL, ignore.strand = TRUE, verbose = FALSE)

Arguments

`signal`	A GRange object carrying the sites of interest.
`gr`	A GRange object carrying the regions of interest.
`ignore.strand`	When set to TRUE, the strand information is ignored in the overlap calculations.
`verbose`	Logical. Default is TRUE. If TRUE, then the progress of the computational tasks is given.

Details

Given a GRanges object 'signal' carrying an arbitrary signal on each range, this function counts the number of sites inside the the given genomic regions 'gr'.

Value

A GRanges object with the genomic regions that carry signals and the number of sites on them.

Author(s)

Robersy Sanchez. https://genomaths.com

Examples

library(GenomicRanges)
some.signal <- makeGRangesFromDataFrame(data.frame(chr = 'chr1', 
                                                   start = 1:15,
                                                   end = 1:15,
                                                   strand = '*'))

some.regions <- makeGRangesFromDataFrame(data.frame(chr = 'chr1', 
                                                    start = c(2, 8),
                                                    end = c(7, 14),
                                                    strand = '*'))

countSignal(signal = some.signal, gr = some.regions)

genomaths/MethylIT.utils documentation built on July 4, 2023, 12:05 a.m.