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cn.farms (version 1.20.0)

cn.FARMS - factor analysis for copy number estimation

Description

This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.

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Version

Version

1.20.0

License

LGPL (>= 2.0)

Maintainer

Andreas Mitterecker

Last Published

February 15th, 2017

Functions in cn.farms (1.20.0)

cn.farms

cn.farms
normalizeCels

Wrapper for the normalization functions
flcSnp6Std

Does a fragment length correction on intensities
flcStd

Does a fragment length correction on intensities
createAnnotation

Creation of annotation files
normalizeNpData

Processes the non-polymorphic data
normalizeQuantiles

Normalization Quantiles
summarizeWindowBps

Combines neighbouring locations to windows
createMatrix

Creates the needed matrix
plotSmoothScatter

Creates a smooth scatter plot
normalizeSor

Runs the SOR normalization on microarray data
cnLibrary

This function was taken from snowfall and edited due to some deprecated function calls.
summarizeFarmsVariational

Summarization variational Laplacian approach
sparseFarmsC

Normalizes the data with SOR
slSummarization

Method for computation of the single-locus summarization
summarizeFarmsExact3

Summarization Laplacian approach with exact computation
normalizeAverage

Scales the range of the non-polymorphic data to the range of a given array.
mlSummarization

Method for computation of the multi-loci summarization
summarizeFarmsGaussian

Summarization Gaussian approach
plotViolines

Create a violine plot
normalizeNone

Runs the SOR normalization on microarray data
combineData

Combine two ExpressionSet objects
plotDensity

Function to create a density plot
summarizeFarmsExact2

Summarization Laplacian approach with exact computation
summarizeFarmsStatistics

Mean or median instead of the FARMS model
getFragmentSet

Finds SNPs which belong to one fragment
getSingleProbeSetSize

Combines data for probeset summarization
summarizeFarmsExact

Summarization Laplacian approach with exact computation
plotEvalIc

Creates a plot with known regions and a numeric vector
plotDendrogram

Plots a dendrogram
distributionDistance

Computes the distribution distance
normAdd

Extracts info from the package name
normalizeSequenceEffect

Correction for probe sequence effects
summarizeWindowMethods

Lists methods for possible window methods
plotRegions

Plots given regions by segments
fragLengCorr

Does a fragment length correction
summarizeFarmsMethods

Lists methods for possible FARMS summarization
dnaCopySf

Runs DNAcopy in parallel mode
doCnFarmsSingle

Does the whole cn.farms process in one call
callSummarize

Defines which variables should be written back when calling a cn.farms run
summarizeWindowStd

Combines neighbouring locations to windows