Package 'oligo' - Bioconductor

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38 snprmasequenceDesignMatrixCreate design matrix for sequencesDescriptionCreates design matrix for sequences.UsagesequenceDesignMatrix(seqs)Argumentsseqscharacter vector of 25-mers.DetailsValueThis assumes all sequences are 25bp long.The design matrix is often used when the objecive is to adjust intensities by sequence.Matrix with length(seqs) rows and 75 columns.ExamplesgenSequence
summarize 39ArgumentsValueobjectSnpFeatureSet objectverbose Verbosity flag. logicalnormalizeToHapmapinternalA SnpQSet object.summarizeTools for microarray preprocessing.DescriptionUsageThese are tools to preprocess microarray data. They include background correction, normalizationand summarization methods.backgroundCorrectionMethods()normalizationMethods()summarizationMethods()backgroundCorrect(object, method=backgroundCorrectionMethods(), copy=TRUE, extra, subset=NULL, targetsummarize(object, probes=rownames(object), method="medianpolish", verbose=TRUE, ...)normalize(object, method=normalizationMethods(), copy=TRUE, subset=NULL,target=core, verbose=TRUE, ..normalizeToTarget(object, targetDist, method="quantile", copy=TRUE, verbose=TRUE)ArgumentsobjectmethodtargetDistprobescopysubsettargetextraverboseObject containing probe intensities to be preprocessed.String determining which method to use at that preprocessing step.Vector with the target distributionCharacter vector that identifies the name of the probes represented by the rowsof object.Logical flag determining if data must be copied before processing (TRUE), or ifdata can be overwritten (FALSE).Not yet implemented.One of the following values: ’core’, ’full’, ’extended’, ’probeset’. Used onlywith Gene ST and Exon ST designs.Extra arguments to be passed to other methods.Logical flag for verbosity.... Arguments to be passed to methods.
Page 1 and 2: Package ‘oligo’May 22, 2014Vers
Page 3 and 4: oligo-package 3snprma . . . . . . .
Page 5 and 6: asicRMA 5ValueA list with the follo
Page 7 and 8: chromosome 7DetailsThe ’transfo
Page 9 and 10: darkColors 9darkColorsCreate set of
Page 11 and 12: getAffinitySplineCoefficients 11See
Page 13 and 14: getCrlmmSummaries 13getCrlmmSummari
Page 15 and 16: getPlatformDesign 15getPlatformDesi
Page 17 and 18: hist 17Examples## Not run:x
Page 19 and 20: justSNPRMA 19justSNPRMASummarizatio
Page 21 and 22: MAplot 21groups, refSamples, which,
Page 23 and 24: mmindex 23DetailsFor all objects bu
Page 25 and 26: oligoPLM-class 25ArgumentsDetails..
Page 27 and 28: paCalls 27Examples## TODO: review c
Page 29 and 30: plotM-methods 29head(dabgP) ## for
Page 31 and 32: pmStrand 31ArgumentsobjectAffySNPPD
Page 33 and 34: ead.xysfiles 33DetailsWhen using
Page 35 and 36: eadSummaries 35readSummariesRead su
Page 37: unDate 37ReferencesRafael. A. Iriza
Page 41 and 42: Index∗Topic IOread.celfiles, 32re
Page 43 and 44: INDEX 43manufacturer,oligoPLM-metho
Page 45: INDEX 45runDate-methods (runDate),

Package 'oligo' - Bioconductor

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