pluginVariation {countprop}

Plugin Variation

Description

Estimates the variation matrix of count-compositional data based on a the same approximation used in logitNormalVariation() only for this function it uses empirical estimates of mu and Sigma. Also performs zero-imputation using cmultRepl() from the zCompositions package.

Usage

pluginVariation(
  counts,
  type = c("standard", "phi", "phis", "rho"),
  order = c("second", "first"),
  impute.zeros = TRUE,
  ...
)

Arguments

counts

Matrix of counts; samples are rows and features are columns.

type

Type of variation metric to be calculated: standard, phi, phis (a symmetrical version of phi), rho, or logp (the variance-covariance matrix of log-transformed proportions).

order

The order of the Taylor-series approximation to be used in the estimation

impute.zeros

If TRUE, then cmultRepl() from the zCompositions package is used to impute zero values in the counts matrix.

...

Optional arguments passed to zero-imputation function cmultRepl()

Value

An estimate of the requested metric of proportionality.

Examples

data(singlecell)

pluginVariation(singlecell)
pluginVariation(singlecell, type="phi")
pluginVariation(singlecell, type="rho")