CAMDAC tumor-normal pipeline — pipeline • CAMDAC

Run CAMDAC analysis on a bulk tumor and patient-matched tissue-matched tumor-adjacent normal sample.

pipeline(tumor, germline = NULL, infiltrates = NULL, origin = NULL, config)

Arguments

tumor: Tumor CamSample object for deconvultion.
germline: Patient-matched normal CamSample object. May be NULL if tumor has CNA calls already.
infiltrates: Normal CamSample as a proxy for infiltrating normal methylation.
origin: Normal CamSample representing cell of origin for tumor-normal differential methylation.
config: Configuration built with CamConfig().