The domino linkage summary class

The linkage summary class contains linkages established in multiple domino objects through gene regulatory network inference and reference to receptor- ligand data bases. A data frame summarizing meta features that describe the domino objects compared in the linkage summary facilitates comparisons of established linkages and differential signaling interactions across categorical sample covariates.

Value

an instance of class linkage_summary

Slots

subject_names

unique names for each domino result included in the summary

subject_meta

data.frame with each row describing one subject and columns describing features of the subjects by which to draw comparisons of signaling networks

subject_linkages

nested list of linkages inferred for each subject. Lists are stored in a heirarchical structure of subject-cluster-linkage where linkages include transcription factors (tfs), linkages between transcription factors and receptors (tfs_rec), active receptors (rec), possible receptor-ligand interactions (rec_lig), and incoming ligands (incoming_lig)