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<< /S /GoTo /D (section.1) >>
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4 0 obj
(Overview)
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5 0 obj
<< /S /GoTo /D (section.2) >>
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8 0 obj
(Data)
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9 0 obj
<< /S /GoTo /D (section.3) >>
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12 0 obj
(Examples)
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13 0 obj
<< /S /GoTo /D (subsection.3.1) >>
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16 0 obj
(Creating aCGH object from log2.ratios and clone info files)
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17 0 obj
<< /S /GoTo /D (subsection.3.2) >>
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20 0 obj
(Filtering and imputation for objects of class aCGH)
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21 0 obj
<< /S /GoTo /D (subsection.3.3) >>
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24 0 obj
(Printing, summary and basic plotting \(fig. 1\) for objects of class aCGH)
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25 0 obj
<< /S /GoTo /D (subsection.3.4) >>
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28 0 obj
(Reading Sproc files)
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29 0 obj
<< /S /GoTo /D (subsection.3.5) >>
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32 0 obj
(Basic plot for batch of aCGH Sproc files. \(fig. 2\))
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33 0 obj
<< /S /GoTo /D (subsection.3.6) >>
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36 0 obj
(Subsetting example)
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37 0 obj
<< /S /GoTo /D (subsection.3.7) >>
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40 0 obj
(Basic plot for the ordered log2 ratios along the genome)
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41 0 obj
<< /S /GoTo /D (subsection.3.8) >>
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44 0 obj
(Computing and plotting hmm states)
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45 0 obj
<< /S /GoTo /D (subsection.3.9) >>
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48 0 obj
(Plotting summary of the tumor profiles)
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49 0 obj
<< /S /GoTo /D (subsection.3.10) >>
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52 0 obj
(Overall frequency plot \(fig. 5\))
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<< /S /GoTo /D (subsection.3.11) >>
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56 0 obj
(Testing association of clones with categorical, censored or continuous outcomes.)
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<< /S /GoTo /D (subsection.3.12) >>
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60 0 obj
(Clustering samples)
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61 0 obj
<< /S /GoTo /D (section.4) >>
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64 0 obj
(Acknowledgements)
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<< /S /GoTo /D [66 0 R /Fit] >>
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