estimates: Extract estimates of the fitted MOSAiCS model

In dongjunchung/mosaics: MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

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)

dongjunchung/mosaics documentation built on March 1, 2020, 3:44 a.m.