Cicero connections to links — ConnectionsToLinks • Signac

Convert the output of Cicero connections to a InteractionSet::GInteractions() object.

Usage

ConnectionsToLinks(conns, ccans = NULL, threshold = 0)

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.

See the Cicero package for more information: https://bioconductor.org/packages/cicero/