README.md

In sbuechler/BCCSclassifier: Breast Cancer Consensus Subtype Classifier

BCCSclassifier

Overview

BCCSclassifier identifies the Breast Cancer Consensus Subtypes (BCCS) of breast cancer samples based on the expression values of genes as published in Horr, C., Buechler, S. Breast Cancer Consensus Subtypes: A system for subtyping breast cancer tumors based on gene expression. npj Breast Cancer. (2021). The package is for research use only, and expects that expression values were obtained from fresh-frozen primary tumor samples.

Installation

After installing the devtools package, BCCSclassifier can be installed by

devtools::install_github("sbuechler/BCCSclassifier", build_vignettes = TRUE)

Basic usage

The BCCS classifications of a dataset of breast cancer samples can be computed with the predict_bccs function. predict_bccs takes as arguments:

dat - a matrix of gene expression values for a dataset of breast cancer samples, with sample identifiers as column names and gene symbols as row names, and

model - one of the strings "erpos", "erneg", "erposneg", depending on the subtyping model with which the samples should be analyzed.

predict_bccs can be used for a large dataset of samples or a single sample. Other requirements on the expression matrix are described in vignette("BCCSclassifier").

predict_bccs returns a data.frame (more precisely, a tibble) with columns sample, subtype_prediction (the predicted classification of the sample), and frequency (the fraction of kTSP models in the family that classified the sample into this subtype).

Much more on the functions underlying predict_bccs can be found in vignette("BCCSclassifier") and documentation for these component functions.

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