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2
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1
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2 # obtained from importing bin-level data obtained from perl codes
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3
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4 setClass( Class="BinData",
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5 representation=representation(
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6 chrID="character",
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7 coord="numeric",
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8 tagCount="numeric",
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9 mappability="numeric",
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10 gcContent="numeric",
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11 input="numeric",
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12 dataType="character"
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13 )
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14 )
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15
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16 # obtained from MOSAiCS Z0 & Z1 model fit
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17
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18 setClass( Class="MosaicsFitEst",
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19 representation=representation(
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20 pi0="numeric",
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21 a="numeric",
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22 betaEst="numeric",
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23 muEst="numeric",
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24 pNfit="list",
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25 b="numeric",
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26 c="numeric",
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27 p1="numeric",
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28 b1="numeric",
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29 c1="numeric",
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30 b2="numeric",
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31 c2="numeric",
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32 inputTrunc="numeric",
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33 analysisType="character"
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34 )
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35 )
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36
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37 setClass( Class="MosaicsFitParam",
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38 representation=representation(
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39 k="numeric",
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40 meanThres="numeric",
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41 s="numeric",
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42 d="numeric"
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43 )
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44 )
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45
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46 setClass( Class="MosaicsFit",
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47 representation=representation(
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48 mosaicsEst="MosaicsFitEst",
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49 mosaicsParam="MosaicsFitParam",
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50 chrID="character",
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51 coord="numeric",
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52 tagCount="numeric",
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53 mappability="numeric",
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54 gcContent="numeric",
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55 input="numeric",
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56 bic1S="numeric",
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57 bic2S="numeric"
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58 )
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59 )
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60
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61 # obtained from final MOSAiCS peak calling
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62
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63 setClass( Class="MosaicsPeakParam",
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64 representation=representation(
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65 analysisType="character",
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66 signalModel="character",
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67 FDR="numeric",
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68 maxgap="numeric",
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69 minsize="numeric",
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70 thres="numeric"
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71 )
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72 )
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73
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74 setClass( Class="MosaicsPeak",
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75 representation=representation(
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76 peakList="data.frame",
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77 peakParam="MosaicsPeakParam",
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78 bdBin="data.frame",
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79 empFDR="numeric"
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80 )
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81 )
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