Package 'charm' - Bioconductor

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40 validatePd Value If the input data frame is valid: a list containing the fileNameColumn, sampleNameColumn and groupColumn. If the input data frame is invalid: FALSE Author(s) See Also Martin Aryee readCharm Examples # See dmrFdr
Index bgAdjust, 2 clusterMaker, 3 cmdsplot, 4 controlQC, 5 countGC, 6 cpgdensity, 7 dmrFdr, 4, 5, 8, 16, 17, 29, 38 dmrFind, 3, 9, 16, 27, 28, 32, 37 dmrFinder, 4, 5, 8, 13, 17, 29, 35, 38 dmrPlot, 8, 16, 38 getControlIndex, 17 maxDensity, 18 methp, 16, 19, 22–24, 35 methPercent, 21 normalizeBetweenSamples, 22 normalizeWithinSamples, 23 plotDensity, 24 plotDMRs, 3, 12, 17, 26, 28, 32, 37 plotRegions, 3, 12, 27, 27, 32, 37, 38 pmQuality, 29 qcReport, 30 qval, 8, 12, 27, 28, 31 readCharm, 6, 16, 20, 34, 40 regionMatch, 36 regionPlot, 4, 5, 8, 17, 29, 37 spatialAdjust, 38 validatePd, 39 41
Page 1 and 2: Package ‘charm’ May 17, 2014 Ty
Page 3 and 4: clusterMaker 3 Value a TilingFeatur
Page 5 and 6: controlQC 5 controlQC Boxplots of c
Page 7 and 8: cpgdensity 7 cpgdensity Get CpG den
Page 9 and 10: dmrFind 9 Examples if (require(char
Page 11 and 12: dmrFind 11 use.limma smoo k SPAN DE
Page 13 and 14: dmrFinder 13 dmrFinder Find differe
Page 15 and 16: dmrFinder 15 p l chr pos pns index
Page 17 and 18: getControlIndex 17 plotG dat buffer
Page 19 and 20: methp 19 Details This function find
Page 21 and 22: methPercent 21 Examples # See dmrFd
Page 23 and 24: normalizeWithinSamples 23 Value a T
Page 25 and 26: plotDensity 25 Arguments dat rx con
Page 27 and 28: plotRegions 27 panel3 G seq if pane
Page 29 and 30: pmQuality 29 Examples # See qval pm
Page 31 and 32: qval 31 Author(s) Martin Aryee Exa
Page 33 and 34: qval 33 Examples ## See vignette. i
Page 35 and 36: eadCharm 35 Arguments files a vecto
Page 37 and 38: egionPlot 37 See Also dmrFind, plot
Page 39: validatePd 39 Details Value The arr

Package 'charm' - Bioconductor

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