crosstalkr {crosstalkr}

crosstalkr: A package for the identification of functionally relevant subnetworks from high-dimensional omics data.

Description

crosstalkr provides a key user function, compute_crosstalk as well as several additional functions that assist in setup and visualization (under development).

crosstalkr functions

compute_crosstalk calculates affinity scores of all proteins in a network relative to user-provided seed proteins. Users can use the human interactome or provide a network represented as an igraph object.

sparseRWR performs random walk with restarts on a sparse matrix. Compared to dense matrix implementations, this should be extremely fast.

bootstrap_null Generates a null distribution based on n calls to sparseRWR

setup_init manages download and storage of interactome data to speed up future analysis

plot_ct allows users to visualize the subnetwork identified in compute_crosstalk. This function relies on the ggraph framework. Users are encouraged to use ggraph or other network visualization packages for more customized figures.

crosstalk_subgraph converts the output of compute_crosstalk to a tidygraph object containing only the identified nodes and their connections to the user-provided seed_proteins. This function also adds degree, degree_rank, and seed_label as attributes to the identified subgraph to assist in plotting.