Package 'charm' - Bioconductor

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6 countGC Examples # See dmrFdr countGC Count probe GC content Description Return the GC content for each probe Usage countGC(dat, type = "pm", idx) Arguments dat type Details a TilingFeatureSet object pm or bg probes idx An optional vector of probe indices for which to return GC content. If not specified, values for all pm (or bg) probes will be returned. This function returns the sum of #G + #C in the pm or bg probes. Value a numeric vector Author(s) Martin Aryee See Also readCharm Examples if (require(charmData)) { phenodataDir
cpgdensity 7 cpgdensity Get CpG density for genomic regions Description Calculate the CpG density for a set of windows Usage cpgdensity(subject, chr, pos, windowSize = 500, sequence = "CG") Arguments subject chr pos windowSize sequence BSGenome object (e.g. Hsapiens) character vector numeric vector number value character string Details Calculate the CpG density for a set of regions. chr and pos specify the region mid-points and windowSize specifies the size of the window to be centered on these mid-points. i.e. The window will stretch from pos-windowSize/2 to pos+windowSize/2. Value a numeric vector Author(s) Martin Aryee Examples if (require(BSgenome.Hsapiens.UCSC.hg18)){ chr
Page 1 and 2: Package ‘charm’ May 17, 2014 Ty
Page 3 and 4: clusterMaker 3 Value a TilingFeatur
Page 5: controlQC 5 controlQC Boxplots of c
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 and 40: validatePd 39 Details Value The arr
Page 41: Index bgAdjust, 2 clusterMaker, 3 c

Package 'charm' - Bioconductor

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