cn.farms - Factor Analysis for copy number estimation

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Documentation for package ‘cn.farms’ version 1.1.12

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callSummarize Defines which variables should be written back
combineData Combine two ExpressionSet objects
createAnnotation Creation of annotation files
createMatrix Creates the needed matrix
distributionDistance Computes the distribution distance
dnaCopySf Runs DNAcopy in parallel mode
doCnFarmsSingle Does the whole cn.farms process in one call
flcSnp6Std Does a fragment length correction on intensities
flcStd Does a fragment length correction on intensities
fragLengCorr Does a fragment length correction
getFragmentSet Finds SNPs which belong to one fragment
getSingleProbeSetSize Combines data for probeset summarization
mlSummarization Does summarization
normAdd Extracts info from the package name
normalizeAverage Scales the range of the non-polymorphic data to the range of a given array.
normalizeCels Wrapper for the normalization functions
normalizeNpData Processes the non-polymorphic data
normalizeQuantiles Normalization Quantiles
normalizeSor Runs the SOR normalization on microarray data
plotDendrogram Plots a dendrogram
plotDensity Function to create a density plot
plotEvalIc Creates a plot with known regions and a numeric vector
plotRegions Plots given regions by segments
plotSmoothScatter Creates a smooth scatter plot
plotViolines Create a violine plot
slSummarization Method for computation of the single-locus summarization
sparseFarmsC Normalizes the data with SOR
summarizeFarmsExact Summarization Laplacian approach with exact computation
summarizeFarmsGaussian Summarization Gaussian approach
summarizeFarmsMethods Lists methods for possible FARMS summarization
summarizeFarmsStatistics Mean or median instead of the FARMS model
summarizeFarmsVariational Summarization variational Laplacian approach
summarizeWindowBps Combines neighbouring locations to windows
summarizeWindowMethods Lists methods for possible window methods
summarizeWindowStd Combines neighbouring locations to windows