shrinkByKappa: Calculate conditions numbers for signature subsets

In yxinyi2/ADAPTS1.0.3: Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

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)

yxinyi2/ADAPTS1.0.3 documentation built on Aug. 5, 2020, 12:09 a.m.