cn.FARMS - factor analysis for copy number estimation

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Documentation for package ‘cn.farms’ version 1.53.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Code demos. Use demo() to run them.

Help Pages

callSummarize	Defines which variables should be written back when calling a cn.farms run
cn.farms	cn.farms
cnLibrary	This function was taken from snowfall and edited due to some deprecated function calls.
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	Method for computation of the multi-loci 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
normalizeNone	Runs the SOR normalization on microarray data
normalizeNpData	Processes the non-polymorphic data
normalizeQuantiles	Normalization Quantiles
normalizeSequenceEffect	Correction for probe sequence effects
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
summarizeFarmsExact2	Summarization Laplacian approach with exact computation
summarizeFarmsExact3	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