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1 \name{export}
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2 \alias{export}
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3 \alias{export,MosaicsPeak-method}
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4 \title{
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5 Export peak calling results to text files
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6 }
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7 \description{
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8 Export peak calling results to text files in TXT, BED, or GFF file formats.
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9 }
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10 \usage{
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11 export(object, ...)
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12 \S4method{export}{MosaicsPeak}( object, type=NA, filename=NA )
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13 }
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14 \arguments{
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15 \item{object}{Object of class \code{MosaicsPeak},
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16 peak calling results obtained using method \code{mosaicsPeak}. }
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17 \item{type}{Format of the exported file.
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18 Possible values are \code{"txt"}, \code{"bed"}, and \code{"gff"}. See Details. }
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19 \item{filename}{Name of the exported file. }
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20 \item{...}{ Other parameters to be passed through to generic \code{export}.}
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21 }
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22 \details{
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23 TXT file format (\code{type="txt"}) exports peak calling results in the most informative way.
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24 Columns include chromosome ID, peak start position, peak end position, peak width,
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25 average posterior probability, minimum posterior probability,
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26 average ChIP tag count, maximum ChIP tag count (always),
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27 average input tag count, average input tag count scaled by sequencing depth,
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28 average log base 2 ratio of ChIP over input tag counts
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29 (if matched control sample is also provided),
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30 average mappability score, and average GC content score
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31 (when mappability and GC content scores are used in the analysis) in each peak.
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32 \code{type="bed"} and \code{type="gff"} export peak calling results in standard BED and GFF file formats,
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33 respectively, where score is the average ChIP tag counts in each peak.
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34 If no peak is detected, \code{export} method will not generate any file.
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35 }
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36 \references{
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37 Kuan, PF, D Chung, 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{\linkS4class{MosaicsPeak}}.
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44 }
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45 \examples{
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46 \dontrun{
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47 library(mosaicsExample)
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48 data(exampleFit)
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49
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50 examplePeak <- mosaicsPeak( exampleFit, signalModel = "2S", FDR = 0.05 )
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51 export( examplePeak, type = "txt", filename = "./TSpeakList.txt" )
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52 export( examplePeak, type = "bed", filename = "./TSpeakList.bed" )
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53 export( examplePeak, type = "gff", filename = "./TSpeakList.gff" )
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54 }
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55 }
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56 \keyword{models}
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57 \keyword{methods}
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