fitNULL {PANR} | R Documentation

## Fit the NULL component of a three-beta mixture model for functional gene associations

### Description

The function performs permutations to the input rich phenotyping screens, and subsequently fit a beta distribution to the densities.

### Usage

    fitNULL(object, nPerm=20, thetaNULL=c(alphaNULL=4, betaNULL=4),
    sumMethod="median", permMethod="keepRep", verbose=TRUE, ...)

### Arguments

`object` | an object of S4 class `BetaMixture`.
`nPerm` | a positive numeric or integer value specifying the number of permutations.
`thetaNULL` | a list of numeric values giving the initial values for estimating the two shape parameters (see `dbeta` for more details).
`sumMethod` | a character value specifying how to summarize estimated parameters from multiple permutations. The current version only supports 'median' and 'mean'.
`permMethod` | a character value of the method to permute, either 'keepRep' (keep the order of replicates) or 'all' (regardless of replicates).
`verbose` | a logical value to switch on (if `TRUE`) or off if `FALSE` detailed run-time message.
`...` | other arguments for function `fitdistr`.

### Details

This function is a step prior to the three-beta mixture model fitting to functional gene association scores. The fitted parameters are then used as a fixed parameters in the three-beta mixture model for further fitting to the real screens. The NULL fitting is performed using the function `fitdistr`, so other arguments for the function fitdistr are also allowed by the argument `...`.

### Value

This function will return an updated object of class `BetaMixture`.

### Author(s)

Xin Wang xw264@cam.ac.uk

### References

Xin Wang, Mauro Castro, Klaas W. Mulder and Florian Markowetz, Posterior association networks and enriched functional gene modules inferred from rich phenotypic perturbation screens, in preparation.

### See Also

`fitBM`

### Examples

    data(Bakal2007)
    bm1<-new("BetaMixture", pheno=Bakal2007, model="global", order=1)
    bm1<-fitNULL(bm1, nPerm=10, thetaNULL=c(alphaNULL=4, betaNULL=4),
    sumMethod="median", permMethod="all", verbose=TRUE)

[Package PANR version 1.40.0 Index]