View source: R/MakeSigMatrix.R
shrinkByKappa | R Documentation |
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
shrinkByKappa( sigMatrix, numChunks = NULL, verbose = TRUE, plotIt = TRUE, singleCore = FALSE, fastStop = TRUE )
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) |
A list with condition numbers and gene lists
library(ADAPTS) LM22 <- ADAPTS::LM22 sigGenesList <- shrinkByKappa(sigMatrix=LM22[1:100,1:5], numChunks=4, verbose=FALSE, plotIt=FALSE, singleCore=TRUE, fastStop=TRUE)
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