RefFreeEWAS (version 2.2)

deviance.RefFreeCellMix: deviance.RefFreeCellMix

Description

Deviance method for objects of type RefFreeCellMix.

Usage

# S3 method for RefFreeCellMix
deviance(object, Y, Y.oob=NULL, EPSILON=1E-9,
  bootstrapIterations=0, bootstrapIndices=NULL, ...)

Arguments

object

RefFreeCellMix object to summarize

Y

Methylation matrix on which x was based

Y.oob

Alternate ("out-of-box") methylation matrix for which to calculate deviance, based on x

EPSILON

Minimum value of variance (zero variances will be reset to this value)

bootstrapIterations

Number of RefFreeCellMix iterations to use in bootstrap (see details)

bootstrapIndices

Bootstrap indices (see details)

…

(Unused).

Details

Deviance based on normal distribution applied to errors of Y after accounting for cell mixture effect, Mu Omega^T. Since RefFreeCellMix does not save the original data Y in the resulting object x, Y must be supplied here. However, deviance may be calculated for an alternative "out-of-bag" methylation matrix, Y.oob. If bootstrapIterations=0, this is what is done. If bootstrapIterations>0, then x$Mu is used to initialize a new value of x via RefFreeCellMix executed on a bootstrap sample of Y with the number of indicated iterations. If bootstrapIndices is provided, the bootstrap will be based on these indices, otherwise the indices will be sampled randomly with replacement from 1:ncol(Y). See RefFreeCellMix for example.