computePCsWithResampling: Compute PCs.

In cavei/houseOfClipUtility: Clip Legacy Functions

Description

For internal use only. Performs Principal Componenent analysis.

Usage

computePCsWithResampling(resampling, exp, shrink = FALSE,
  method = c("regular", "topological", "sparse"), cliques = NULL,
  maxPCs = 3)

Arguments

resampling	list of resampled columns
exp	a matrix
shrink	logical, whether to shrink or not.
method	one of 'regular', 'topological' and 'sparse'
cliques	the pathway topology summarized in a list of cliques
maxPCs	the maximum number of PCs to consider

Details

Three methods are implemented: * regular: a regular PCA ('prcomp') * topological: PCA using a pathway topology. * sparse: sparse PCA analysis implemented by 'elasticnet'

Value

a list with the following elements:

x	the computed PCs
sdev	the standard deviation captured by the PCs
loadings	the loadings

Examples

  fakeExp <- randomExpression(4)
  computePCs(t(fakeExp))

cavei/houseOfClipUtility documentation built on May 12, 2019, 5:23 p.m.