ml_subtype {OncoSubtype}

Predict the subtypes of selected cancer type using machine learning

Description

Predict the subtypes of selected cancer type using machine learning

Usage

ml_subtype(
  data,
  disease = "LUSC",
  method = "rf",
  removeBatch = TRUE,
  seed = NULL
)

Arguments

data

data set to predict the subtypes which is a numeric matrix with row names of features and column names of samples

disease

character string of the disease to predict subtypes, currently support 'LUSC', 'LUAD', and 'BLCA'.

method

character string of the method to use currently support 'rf'.

removeBatch

whether do batch effect correction using limma::removeBatchEffect, default TRUE.

seed

integer seed to use.

Value

An object of class "SubtypeClass" with four slots: genes used for predictiong, predicted subtypes of samples, a matrix of predicting scores, and the method.

References

1. Wilkerson MJ, Yin X, Hayes D, et al. (2010). “Lung Squamous Cell Carcinoma mRNA Expression Subtypes Are Reproducible, Clinically Important, and Correspond to Normal Cell Types.” Clin Cancer Res, 16(19), 4864-4875.

2. Wilkerson MJ, Yin X, Hayes D, et al. (2012). “Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation.” Plos One, 7(5), e36530.

3. Network TCGA (2015). “Comprehensive genomic characterization of head and neck squamous cell carcinomas.” Nature, 517, e36530.

Examples

## Not run: 
library(OncoSubtype)
data <- get_median_centered(example_fpkm)
data <- assays(data)$centered
rownames(data) <- rowData(example_fpkm)$external_gene_name
ml_subtype(data, disease = 'LUAD', method = 'rf', seed = 123)

## End(Not run)