ConnectionsToLinks: Cicero connections to links
In timoast/signac: Analysis of Single-Cell Chromatin Data

ConnectionsToLinks

R Documentation

Cicero connections to links

Description

Convert the output of Cicero connections to a set of genomic ranges where the start and end coordinates of the range are the midpoints of the linked elements. Only elements on the same chromosome are included in the output.

Usage

ConnectionsToLinks(conns, ccans = NULL, threshold = 0, sep = c("-", "-"))

Arguments

`conns`	A dataframe containing co-accessible elements. This would usually be the output of `run_cicero` or `assemble_connections`. Specifically, this should be a dataframe where the first column contains the genomic coordinates of the first element in the linked pair of elements, with chromosome, start, end coordinates separated by "-" characters. The second column should be the second element in the linked pair, formatted in the same way as the first column. A third column should contain the co-accessibility scores.
`ccans`	This is optional, but if supplied should be a dataframe containing the cis-co-accessibility network (CCAN) information generated by `generate_ccans`. Specifically, this should be a dataframe containing the name of the peak in the first column, and the CCAN that it belongs to in the second column.
`threshold`	Threshold for retaining a coaccessible site. Links with a value less than or equal to this threshold will be discarded.
`sep`	Separators to use for strings encoding genomic coordinates. First element is used to separate the chromosome from the coordinates, second element is used to separate the start from end coordinate.