classifyCMString: classification of sample gene expression profiles into...

In rpiskol/CMString: CMS classification using a selected set of genes that are profiled using the NanoStrin echnology

Description

classification of sample gene expression profiles into consensus molecular subtypes (CMS)

Usage

classifyCMString(x, applylog = TRUE, mediancenter = TRUE, zScore = TRUE,
  s.stat = "lambda.min", thresh = NULL)

Arguments

x	ExpressionSet object or gene expression matrix for samples (rows) and genes (columns) [default: none]
applylog	boolean specifying whether log2 transformation should be applied to the data [default: TRUE]
mediancenter	boolean specifying whether expression of single genes should be median centered [default: TRUE]
zScore	boolean specifying whether gene expression should be z-scored [default: TRUE]
s.stat	Value of the penalty parameter lambda at which prediction will be made [default: lambda.min]
thresh	minimum probability necessary for CMS call [default: NULL - the CMS with highest probability will be reported regardless of its probability]

Value

list with results

Author(s)

Robert Piskol

rpiskol/CMString documentation built on May 24, 2019, 8:52 a.m.