estimates {mosaics} | R Documentation

## Extract estimates of the fitted MOSAiCS model

### Description

Extract estimates from `MosaicsFit` class object, which is a fitted MOSAiCS model.

### Usage

    estimates( object, ... )
    ## S4 method for signature 'MosaicsFit'
    estimates( object )

### Arguments

`object` | Object of class `MosaicsFit`, which represents a fitted MOSAiCS model obtained using method `mosaicsFit`.
`...` | Other parameters to be passed through to generic `estimates`.

### Value

Returns a list with components:

`pi0` | Mixing proportion of background component.
`a` | Parameter for background component.
`betaEst` | Parameter for background component (coefficient estimates).
`muEst` | Parameter for background component.
`b` | Parameter for one-signal-component model.
`c` | Parameter for one-signal-component model.
`p1` | Parameter for two-signal-component model (mixing proportion of signal components).
`b1` | Parameter for two-signal-component model (the first signal component).
`c1` | Parameter for two-signal-component model (the first signal component).
`b2` | Parameter for two-signal-component model (the second signal component).
`c2` | Parameter for two-signal-component model (the second signal component).
`analysisType` | Analysis type. Possible values are "OS" (one-sample analysis), "TS" (two-sample analysis using mappability and GC content), and "IO" (two-sample analysis without using mappability and GC content).

### Author(s)

Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles

### References

Kuan, PF, D Chung, G Pan, JA Thomson, R Stewart, and S Keles (2011), "A Statistical Framework for the Analysis of ChIP-Seq Data", Journal of the American Statistical Association, Vol. 106, pp. 891-903.

Chung, D, Zhang Q, and Keles S (2014), "MOSAiCS-HMM: A model-based approach for detecting regions of histone modifications from ChIP-seq data", Datta S and Nettleton D (eds.), Statistical Analysis of Next Generation Sequencing Data, Springer.

### See Also

`mosaicsFit`, `MosaicsFit`.

### Examples

    ## Not run:
    library(mosaicsExample)
    data(exampleBinData)
    exampleFit <- mosaicsFit( exampleBinData, analysisType="IO" )
    estimates(exampleFit)

    ## End(Not run)

[Package mosaics version 2.28.0 Index]