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Refined COO prediction function

refined_coo_rnaseq.Rd

Wrapper for running coo_normalize, coo_predict, and dzsig_predict

Usage

refined_coo_rnaseq(cds)

Arguments

cds

  • a DESeqDataSet object, with raw counts in the "counts" slot.

Value

a data frame with six columns:

  • Sample names

  • COO LPS score prediction

  • COO class

  • DZsig LPS score prediction

  • DZsig class

  • Refined COO class

Details

This function is a wrapper that runs the normalization and both COO and DZsig predictions, and then combines the results into a single data frame, including the refined COO class. Refined Cell of Origin classification is assigned hierarchically:

  • If ABC, then ABC

  • If DZsig-POS, DZsig-POS

  • Else, COO (GCB or Unclassified)