Annotate GEPs

Annotate the GEPs produced by GBCD using the patient identity information of cells

gep_annotation(L, metadata)

Arguments

L

cell x GEP matrix of GEP membership returned by fit_gbcd.

metadata

data frame containing at least a column “subject” indicating the patient identity of cells. Each row contains a cell and the rownames must match those of L.

Value

A data frame containing GEPs in rows and the following two columns: the column “patient_specific” reflects the degree of patient-specific expression of a GEP, and larger values indicate a GEP is more patient-specific rather than expressed in multiple patients. The column “between_patient_variation” quantifies how strongly a GEP's memberships vary between patients as opposed to within patients, and larger values indicate a GEP has larger between- than within-patient variation.