genomic_corr_jaccard: Jaccard coefficient between two sets of genomic regions

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Jaccard coefficient between two sets of genomic regions

Usage

genomic_corr_jaccard(query, reference, background = NULL)

Arguments

query	genomic region 1, a GRanges object
reference	genomic region 2, a GRanges object
background	background regions that should be only looked in, a GRanges object

Details

Jaccard coefficient is defined as the total length of intersection divided by total length of union of two sets of genomic regions.

You can set the background when calculating Jaccard coefficient. For example, if the interest is the Jaccard coefficient between CpG sites in query and in reference background can be set with a GRanges object which contains positions of CpG sites.

Be careful with the strand in your GRanges object!

Value

A single correlation value.

Author(s)

Zuguang Gu <[e-mail]>

See Also

genomic_regions_correlation

Examples

gr1 = GRanges(seqnames = "chr1", ranges = IRanges(c(1, 5), c(3, 8)))
gr2 = GRanges(seqnames = "chr1", ranges = IRanges(c(2, 6), c(4, 8)))
genomic_corr_jaccard(gr1, gr2)

eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.