%PDF-1.4 % 5 0 obj << /S /GoTo /D (section.1) >> endobj 8 0 obj (Overview) endobj 9 0 obj << /S /GoTo /D (section.2) >> endobj 12 0 obj (Data) endobj 13 0 obj << /S /GoTo /D (section.3) >> endobj 16 0 obj (Examples) endobj 17 0 obj << /S /GoTo /D (subsection.3.1) >> endobj 20 0 obj (Creating aCGH object from log2.ratios and clone info files) endobj 21 0 obj << /S /GoTo /D (subsection.3.2) >> endobj 24 0 obj (Filtering and imputation for objects of class aCGH) endobj 25 0 obj << /S /GoTo /D (subsection.3.3) >> endobj 28 0 obj (Printing, summary and basic plotting \(fig. 1\) for objects of class aCGH) endobj 29 0 obj << /S /GoTo /D (subsection.3.4) >> endobj 32 0 obj (Reading Sproc files) endobj 33 0 obj << /S /GoTo /D (subsection.3.5) >> endobj 36 0 obj (Basic plot for batch of aCGH Sproc files. \(fig. 2\)) endobj 37 0 obj << /S /GoTo /D (subsection.3.6) >> endobj 40 0 obj (Subsetting example) endobj 41 0 obj << /S /GoTo /D (subsection.3.7) >> endobj 44 0 obj (Basic plot for the ordered log2 ratios along the genome) endobj 45 0 obj << /S /GoTo /D (subsection.3.8) >> endobj 48 0 obj (Computing and plotting hmm states) endobj 49 0 obj << /S /GoTo /D (subsection.3.9) >> endobj 52 0 obj (Plotting summary of the tumor profiles) endobj 53 0 obj << /S /GoTo /D (subsection.3.10) >> endobj 56 0 obj (Overall frequency plot \(fig. 5\)) endobj 57 0 obj << /S /GoTo /D (subsection.3.11) >> endobj 60 0 obj (Testing association of clones with categorical, censored or continuous outcomes.) endobj 61 0 obj << /S /GoTo /D (subsection.3.12) >> endobj 64 0 obj (Clustering samples) endobj 65 0 obj << /S /GoTo /D (section.4) >> endobj 68 0 obj (Acknowledgements) endobj 69 0 obj << /S /GoTo /D [70 0 R /Fit ] >> endobj 97 0 obj << /Length 2070 /Filter /FlateDecode >> stream xYrF+xX%gzK$[v"E "iCOoE{tyG&UhrCGI+d6=8`YCi{xQK o((`|7o9b:v&'>W{ynDZ-]܌rpņV&8n~+=m3!mGSmr(H91]3tL%nvf4a8}JWrۮ,
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