refineBasal: Refine basal-like muscle invasive bladder cancer

In xlucpu/refineMIBC: Refine muscle-invasive bladder cancer

Description

Refine pre-identified basal-like muscle invasive bladder cancer into either basal-inflamed or basal-noninflamed subtype based on a random forest classifier.

Usage

refineBasal(
  expr = NULL,
  isBasal = NULL,
  res.path = getwd(),
  res.name = "REFINED_MIBC_BASAL"
)

Arguments

expr	A numeric expression matrix with row features and sample columns.
isBasal	A logic vector to indicate if the sample is basal-like or not. NULL by default and all samples will be assumed as basal-like.
res.path	A string value to indicate the path for saving the prediction result.
res.name	A string value to indicate the name of the output prediction table.

Value

A data.frame storing the random forest prediction results, including 'samID' for sample name, 'prob' for probability as basal-inflamed, and 'basal' for final classifications using 0.5 as cutoff.

Examples

library(refineMIBC)
load(system.file("extdata", "demo.RData", package = "refineMIBC", mustWork = TRUE)) # load example data
expr <- demo$MIBC.expr
subt <- demo$MIBC.subt
isbasal <- subt$TCGA == "Basal_squamous"
iBasal  <- refineBasal(expr    = expr,
                       isBasal = isbasal)
head(iBasal)

xlucpu/refineMIBC documentation built on Jan. 14, 2022, 8:35 p.m.