predict_bccs: BCCS predictor

In sbuechler/BCCSclassifier: Breast Cancer Consensus Subtype Classifier

Description

A function to predict the subtypes of breast cancers with respect to a BCCSclassifier model

Usage

predict_bccs(dat, model)

Arguments

dat

An object of class matrix with samples as column names, gene symbols as row names, and entries the corresponding expression levels. The included tibble bccs_classifier_genes contains the gene symbols and ENTREZIDs used in the BCCSclassifier models, along with Affymetrix (hgu133a) and Illumina (illuminaHuman v3) probes that can be used to represent the associated genes. Expression values must not be scaled or median-centered.

model

A character string that is one of "erposneg", "erpos", "erneg", to determine whether BCCSclassifier(ER+/-), BCCSclassifier(ER+), or BCCSclassifier(ER-) should be used for subtyping.

Details

Learn more in the vignette by executing vignette("BCCSclassifier")

Value

The output is a tibble (data.frame) with columns sample, subtype_prediction, frequency. There is one record for each sample in the column names of dat. frequency is the fraction of kTSP models in the family that predicted the sample was in the finally chosen subtype.

sbuechler/BCCSclassifier documentation built on Dec. 22, 2021, 10:19 p.m.