compare_connections: Compare Cicero connections to other datasets

In cole-trapnell-lab/cicero-release: Predict cis-co-accessibility from single-cell chromatin accessibility data

Compare Cicero connections to other datasets

Description

Compare two sets of connections and return a vector of logicals for whether connections in one are present in the other.

Usage

compare_connections(conns1, conns2, maxgap = 0)

Arguments

conns1	A data frame of Cicero connections, like those output from assemble_connections. The first two columns must be the coordinates of peaks that are connected.
conns2	A data frame of connections to be searched for overlap. The first two columns must be coordinates of genomic sites that are connected.
maxgap	The number of base pairs between peaks allowed to be called overlapping. See findOverlaps-methods in the IRanges package for further description.

Value

A vector of logicals of whether the Cicero pair is present in the alternate dataset.

Examples

## Not run: 
cons$in_dataset <- compare_connections(conns, alt_data)

## End(Not run)

cole-trapnell-lab/cicero-release documentation built on Sept. 4, 2024, 1:49 p.m.