deviance.RefFreeCellMix: deviance.RefFreeCellMix

In RefFreeEWAS: EWAS using Reference-Free DNA Methylation Mixture Deconvolution

Description

Deviance method for objects of type RefFreeCellMix.

Usage

## S3 method for class '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.

RefFreeEWAS documentation built on May 2, 2019, 5:52 a.m.