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1 \name{MosaicsPeak-class}
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2 \Rdversion{1.1}
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3 \docType{class}
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4 \alias{MosaicsPeak-class}
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5 \alias{bdBin,MosaicsPeak-method}
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6 \alias{empFDR,MosaicsPeak-method}
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7 %\alias{export,MosaicsPeak-method}
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8 \alias{print,MosaicsPeak-method}
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9 \alias{show,MosaicsPeak-method}
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10
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11 \title{Class "MosaicsPeak" }
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12 \description{
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13 This class represents peak calling results.
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14 }
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15 \section{Objects from the Class}{
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16 Objects can be created by calls of the form \code{new("MosaicsPeak", ...)}.
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17 }
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18 \section{Slots}{
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19 \describe{
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20 \item{\code{peakList}:}{Object of class \code{"data.frame"}, representing peak list. }
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21 \item{\code{peakParam}:}{Object of class \code{"MosaicsPeakParam"},
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22 representing parameters for peak calling. }
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23 \item{\code{bdBin}:}{Object of class \code{"numeric"},
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24 representing a vector of bounded bins. }
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25 \item{\code{empFDR}:}{Object of class \code{"numeric"},
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26 representing empirical FDR. }
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27 }
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28 }
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29 \section{Methods}{
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30 \describe{
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31 \item{export}{\code{signature(object = "MosaicsPeak")}: export peak list into text files. }
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32 \item{print}{\code{signature(x = "MosaicsPeak")}: return peak list in data frame format. }
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33 \item{show}{\code{signature(object = "MosaicsPeak")}: provide brief summary of the object. }
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34 }
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35 }
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36 \references{
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37 Kuan, PF, D Chung, G Pan, JA Thomson, R Stewart, and S Keles (2011),
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38 "A Statistical Framework for the Analysis of ChIP-Seq Data",
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39 \emph{Journal of the American Statistical Association}, Vol. 106, pp. 891-903.
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40 }
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41 \author{ Dongjun Chung, Pei Fen Kuan, Sunduz Keles }
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42 \seealso{
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43 \code{\link{mosaicsPeak}}, \code{\link{export}}.
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44 }
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45 \examples{
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46 showClass("MosaicsPeak")
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47 \dontrun{
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48 library(mosaicsExample)
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49 data(exampleFit)
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50 examplePeak <- mosaicsPeak( exampleFit, signalModel = "2S", FDR = 0.05 )
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51
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52 examplePeak
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53 print(examplePeak)[1:10, ]
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54 export( examplePeak, type = "txt", filename = "./TSpeakList.txt" )
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55 export( examplePeak, type = "bed", filename = "./TSpeakList.bed" )
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56 export( examplePeak, type = "gff", filename = "./TSpeakList.gff" )
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57 }
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58 }
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59 \keyword{classes}
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