lol.utils.decomp: A utility to use irlba when necessary

Description Usage Arguments Value Author(s)

View source: R/pca.R

Description

A utility to use irlba when necessary

Usage

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lol.utils.decomp(X, xfm = FALSE, xfm.opts = list(), ncomp = 0, t = 0.05,
  robust = FALSE)

Arguments

X

the data to compute the svd of.

xfm

whether to transform the variables before taking the SVD.

  • FALSEapply no transform to the variables.

  • 'unit'unit transform the variables, defaulting to centering and scaling to mean 0, variance 1. See scale for details and optional args.

  • 'log'log-transform the variables, for use-cases such as having high variance in larger values. Defaults to natural logarithm. See log for details and optional args.

  • 'rank'rank-transform the variables. Defalts to breaking ties with the average rank of the tied values. See rank for details and optional args.

  • c(opt1, opt2, etc.)apply the transform specified in opt1, followed by opt2, etc.

xfm.opts

optional arguments to pass to the xfm option specified. Should be a numbered list of lists, where xfm.opts[[i]] corresponds to the optional arguments for xfm[i]. Defaults to the default options for each transform scheme.

ncomp

the number of left singular vectors to retain.

t

the threshold of percent of singular vals/vecs to use irlba.

robust

whether to use a robust estimate of the covariance matrix when taking PCA. Defaults to FALSE.

Value

the svd of X.

Author(s)

Eric Bridgeford


neurodata/lol documentation built on Oct. 17, 2018, 8:58 a.m.