Extract estimates of the fitted MOSAiCS model

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Description

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

Usage

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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

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

## End(Not run)