shrinkByKappa {ADAPTS}

Calculate conditions numbers for signature subsets

Description

Remove genes by chunks by picking those the most improve the condition number. Will set any infinite condition numbers to max(kappas[!is.infinite(kappas)])+1 Return the condition numbers with their gene lists

Usage

shrinkByKappa(
  sigMatrix,
  numChunks = NULL,
  verbose = TRUE,
  plotIt = TRUE,
  singleCore = FALSE,
  fastStop = TRUE
)

Arguments

sigMatrix

The original signature matrix

numChunks

The number of groups of genes to remove (DEFAULT: NULL)

verbose

Print out the current chunk as is it's being calculated (DEFAULT: NULL)

plotIt

The title of the plot (DEFAULT: TRUE)

singleCore

Set to FALSE to use multiple cores to calculate condition numbers (DEFAULT: FALSE)

fastStop

Halt early when the condition number changes by less than 1 for 3 iterations (DEFAULT: FALSE)

Value

A list with condition numbers and gene lists

Examples

library(ADAPTS)
LM22 <- ADAPTS::LM22
sigGenesList <- shrinkByKappa(sigMatrix=LM22[1:100,1:5], numChunks=4, 
verbose=FALSE, plotIt=FALSE, singleCore=TRUE, fastStop=TRUE)