raptorise: raptorise is a wrapper for the compute_risk_score function...

In christianbromley/raptor: Estimating Renal Anti-Pd(l)1 probabiliTy Of Response scores from gene expression data

Description

raptorise is a wrapper for the compute_risk_score function enabling it to be run over all 4 of the models

Usage

raptorise(expr)

Arguments

expr

a data frame of gene expression data with genes as column names and samples as rownames. Ideally expression will be in log2(TPM+1) format. The data frame should also include columns for the MSKCC prognostic score if the data is from renal cancer patients (column name = "mskcc"). Note that the COX-IS model contains two coefficients that are 0. Ignore these. If they are missing they will be printed out as missing, but they aren't affecting the model anyway.

Value

data.frame with variables sample name and a column for each predictor method, with the continuous variable, the stratifier based on log2tpm expression data cutoff, and a stratifier based on the proportion of high/low patients in training.

christianbromley/raptor documentation built on Sept. 1, 2020, 12:05 p.m.