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DZsig prediction function

dzsig_predict.Rd

Function for predicting DZsig using a normalized RNASeq dataset

Usage

dzsig_predict(norm_eset, model)

Arguments

norm_eset

A normalized ExpressionSet, as returned by coo_normalize

model

The fitted DZsig model.

Value

a data frame with three columns:

  • Sample names

  • LPS score prediction

  • DZsig class

Details

This function uses the model generated on the GAMBL dataset to predict Dark Zone Signature (DZsig) on a normalized expression dataset. No subsetting needs to be performed, but the expression matrix must have either refseq (e.g. "geneID:7900") or ENSEMBL (e.g. ENSG....) gene IDs as the rownames. Thresholds used for classification are -15.6 and -6.3, as per the original DLBCL90 publication (Ennishi et al, J Clin Oncol 2019).