Calculate a signaling network for a domino object

This function calculates a signaling network. It requires a domino object preprocessed from create_domino and returns a domino object prepared for plotting with the various plotting functions in this package.

Usage

build_domino(
  dom,
  max_tf_per_clust = 5,
  min_tf_pval = 0.01,
  max_rec_per_tf = 5,
  rec_tf_cor_threshold = 0.15,
  min_rec_percentage = 0.1
)

Arguments

dom

Domino object from create_domino.

max_tf_per_clust

Maximum number of transcription factors called active in a cluster.

min_tf_pval

Minimum p-value from differential feature score test to call a transcription factor active in a cluster.

max_rec_per_tf

Maximum number of receptors to link to each transcription factor.

rec_tf_cor_threshold

Minimum pearson correlation used to consider a receptor linked with a transcription factor. Increasing this will decrease the number of receptors linked to each transcription factor.

min_rec_percentage

Minimum percentage of cells in cluster expressing a receptor for the receptor to be linked to trancription factors in that cluster.

Value

A domino object with a signaling network built

Examples

pbmc_dom_tiny_built <- build_domino(
 dom = dominoSignal:::pbmc_dom_tiny, min_tf_pval = .001, max_tf_per_clust = 25,
 max_rec_per_tf = 25, rec_tf_cor_threshold = .25, min_rec_percentage = 0.1
)