fracOverlap: Retrieve intervals overlapping by fraction of width

In girafe: Genome Intervals and Read Alignments for Functional Exploration

Description

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

Usage

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

   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.