Specify fxn arguments in fitVarPartModel

[marcora]

in fitVarPartModel(E_raw, ~ Disease + Sex + (1|Individual), meta, fxn = summary), is it possible to specify arguments for the summary or whatever other function the user wants to use on the lmerMod fit object passed to it?

[GabrielHoffman]

I just saw this, sorry about the delay.

Consider a toy example where you want to extract the residual standard deviation and add 12. Instead of passing fxn=sigma, create a new function that does what you want

library(variancePartition)     
data(varPartData)

form <- ~ Age + (1 | Individual) + (1 | Tissue)

f = function(fit){
  sigma(fit) + 12
}
fitVarPartModel(geneExpr[1:3,], form, info, fxn=f)