# cn.FARMS - factor analysis for copy number estimation

## Documentation for package ‘cn.farms’ version 1.40.0

- 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