fracOverlap: Retrieve intervals overlapping by fraction of width

Description Usage Arguments Value Author(s) See Also Examples

View source: R/fracOverlap.R

Description

Function to retrieve overlapping intervals that overlap at least by a specified fraction of their widths.

Usage

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fracOverlap(I1, I2, min.frac=0.0, both=TRUE, mem.friendly=FALSE)

Arguments

I1

object that inherits from class Genome_intervals

I2

object that inherits from class Genome_intervals

min.frac

numeric; minimum required fraction of each of the two interval widths by which two intervals should overlap in order to be marked as overlapping.

both

logical; shall both overlap partners meet the minimum fraction min.frac requirement? If FALSE, then overlaps with only partner involved to at least that fraction are also reported.

mem.friendly

logical; if set to TRUE an older but memory-friendlier version of interval_overlap is used inside this function. Note that mem.friendly is only evaluated if I1 or I2 is of class AlignedGenomeIntervals.

Value

An object of class data.frame with one row each for a pair of overlapping elements.

Index1

Index of interval in first interval list

Index2

Index of interval in second interval list

n

number of bases that the two intervals overlap

fraction1

fraction of interval 1's width by which the two intervals overlap

fraction2

fraction of interval 2's width by which the two intervals overlap

Author(s)

J. Toedling

See Also

interval_overlap

Examples

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   data("gen_ints", package="genomeIntervals")
   i[4,2] <- 13L
   fracOverlap(i, i, 0.5)

girafe documentation built on Nov. 8, 2020, 4:56 p.m.