build_intersect: Given a GRangesList object, determine which items overlap...

Description Usage Arguments Value

View source: R/IntersectionHelper.R

Description

Given a GRangesList object, determine which items overlap each others.

Usage

1
build_intersect(grl, keep.signal = FALSE)

Arguments

grl

The GRangesList object whose elements need to be overlapped with each others.

keep.signal

Should the values of signal be kept?

Value

A list with the following elements:

Regions

A GRanges object with all genomic ranges occupied by at least one item. All ranges are "flattened", so if two of the initial ranges overlapped each other imperfectly, they are combined into a single region spanning both of them.

Matrix

A matrix, with ncol= the number of items in the initial GRangesList and nrow= the total number of loci, which is equal to the length of Regions. A value of 1 or more within the matrix indicates that the regions described by the column overlapped the region defined by the row.

List

A list of length(grl) numeric vectors indicating which indices of Regions overlap with the given condition/protein. Useful to translate the regions into unique names for drawing venn diagrams.

Names

The names of the initial grl items, corresponding to the column names of Matrix and the names of the element of List.

Length

The number of items in the initial GRangesList, corresponding to the number of columns in Matrix and the number of elements in List

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ArnaudDroitLab/ef.utils documentation built on Nov. 24, 2018, 5:11 p.m.