cn.farms: cn.FARMS - factor analysis for copy number estimation

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.

AuthorAndreas Mitterecker, Djork-Arne Clevert
Date of publicationNone
MaintainerAndreas Mitterecker <mitterecker@bioinf.jku.at>
LicenseLGPL (>= 2.0)
Version1.22.0
http://www.bioinf.jku.at/software/cnfarms/cnfarms.html

View on Bioconductor

Man pages

callSummarize: Defines which variables should be written back when calling a...

cn.farms: cn.farms

cnLibrary: This function was taken from snowfall and edited due to some...

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...

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

Files in this package

cn.farms/DESCRIPTION
cn.farms/NAMESPACE
cn.farms/R
cn.farms/R/callSummarize.R cn.farms/R/cnFarms.R cn.farms/R/combineData.R cn.farms/R/correctPkgname.R cn.farms/R/createAnnotation.R cn.farms/R/createMatrix.R cn.farms/R/determineBaselineArray.R cn.farms/R/distributionDistance.R cn.farms/R/dnaCopySf.R cn.farms/R/doCnFarms.R cn.farms/R/fragLengthCorr.R cn.farms/R/normAdd.R cn.farms/R/normalizeAverage.R cn.farms/R/normalizeCels.R cn.farms/R/normalizeNone.R cn.farms/R/normalizeNpData.R cn.farms/R/normalizeProbeSequence.R cn.farms/R/normalizeQuantiles.R cn.farms/R/normalizeSor.R cn.farms/R/plotDendrogram.R cn.farms/R/plotDensity.R cn.farms/R/plotEvalIc.R cn.farms/R/plotSmoothScatter.R cn.farms/R/plotViolines.R cn.farms/R/plotsRegions.R cn.farms/R/sFclusterFunctions.R cn.farms/R/sFinit.R cn.farms/R/sFsnowWrappers.R cn.farms/R/sFsnowfall-internal.R cn.farms/R/sFsocketRequest.R cn.farms/R/snowfallExt.R cn.farms/R/sparseFarmsC.R cn.farms/R/summarizationMl.R cn.farms/R/summarizationSl.R cn.farms/R/summarizeFarmsGaussian.R cn.farms/R/summarizeFarmsLaplaceExact.R cn.farms/R/summarizeFarmsLaplaceExact2.R cn.farms/R/summarizeFarmsLaplaceExact3.R cn.farms/R/summarizeFarmsLaplaceVar.R cn.farms/R/summarizeFarmsMethods.R cn.farms/R/summarizeStatistics.R
cn.farms/R/sysdata.rda
cn.farms/R/utils-lds.R cn.farms/R/vanillaIce.R cn.farms/R/windowFunctions.R cn.farms/R/windowMethods.R cn.farms/R/zzz.R
cn.farms/build
cn.farms/build/vignette.rds
cn.farms/demo
cn.farms/demo/00Index
cn.farms/demo/demo01Snp6.R
cn.farms/demo/demo02Snp5.R
cn.farms/demo/demo03Snp500k.R
cn.farms/demo/demo04Snp250k.R
cn.farms/demo/demo05Snp50k.R
cn.farms/demo/demo99Testing.R
cn.farms/inst
cn.farms/inst/CITATION
cn.farms/inst/doc
cn.farms/inst/doc/cn.farms.R
cn.farms/inst/doc/cn.farms.Rnw
cn.farms/inst/doc/cn.farms.pdf
cn.farms/inst/exampleData
cn.farms/inst/exampleData/annotation
cn.farms/inst/exampleData/annotation/pd.genomewidesnp.6
cn.farms/inst/exampleData/annotation/pd.genomewidesnp.6/1.1.0
cn.farms/inst/exampleData/annotation/pd.genomewidesnp.6/1.1.0/featureSet.RData
cn.farms/inst/exampleData/mlData.RData
cn.farms/inst/exampleData/normData.RData
cn.farms/inst/exampleData/slData.RData
cn.farms/inst/exampleData/testSegments.RData
cn.farms/man
cn.farms/man/callSummarize.Rd cn.farms/man/cn.farms.Rd cn.farms/man/cnLibrary.Rd cn.farms/man/combineData.Rd cn.farms/man/createAnnotation.Rd cn.farms/man/createMatrix.Rd cn.farms/man/distributionDistance.Rd cn.farms/man/dnaCopySf.Rd cn.farms/man/doCnFarmsSingle.Rd cn.farms/man/flcSnp6Std.Rd cn.farms/man/flcStd.Rd cn.farms/man/fragLengCorr.Rd cn.farms/man/getFragmentSet.Rd cn.farms/man/getSingleProbeSetSize.Rd cn.farms/man/mlSummarization.Rd cn.farms/man/normAdd.Rd cn.farms/man/normalizeAverage.Rd cn.farms/man/normalizeCels.Rd cn.farms/man/normalizeNone.Rd cn.farms/man/normalizeNpData.Rd cn.farms/man/normalizeQuantiles.Rd cn.farms/man/normalizeSequenceEffect.Rd cn.farms/man/normalizeSor.Rd cn.farms/man/plotDendrogram.Rd cn.farms/man/plotDensity.Rd cn.farms/man/plotEvalIc.Rd cn.farms/man/plotRegions.Rd cn.farms/man/plotSmoothScatter.Rd cn.farms/man/plotViolines.Rd cn.farms/man/slSummarization.Rd cn.farms/man/sparseFarmsC.Rd cn.farms/man/summarizeFarmsExact.Rd cn.farms/man/summarizeFarmsExact2.Rd cn.farms/man/summarizeFarmsExact3.Rd cn.farms/man/summarizeFarmsGaussian.Rd cn.farms/man/summarizeFarmsMethods.Rd cn.farms/man/summarizeFarmsStatistics.Rd cn.farms/man/summarizeFarmsVariational.Rd cn.farms/man/summarizeWindowBps.Rd cn.farms/man/summarizeWindowMethods.Rd cn.farms/man/summarizeWindowStd.Rd
cn.farms/src
cn.farms/src/R_init_cnfarms.c
cn.farms/src/cn.farms.h
cn.farms/src/laplace.cpp
cn.farms/src/sepp_vect.h
cn.farms/src/sparse_farms.c
cn.farms/vignettes
cn.farms/vignettes/bioinf-article.txi
cn.farms/vignettes/bioinf-bar.png
cn.farms/vignettes/bioinf.cls
cn.farms/vignettes/cn.farms.Rnw
cn.farms/vignettes/cnFarmsDefs.sty
cn.farms/vignettes/cnv.bib
cn.farms/vignettes/figures
cn.farms/vignettes/figures/figure1.pdf
cn.farms/vignettes/figures/figure2.pdf
cn.farms/vignettes/natbib.bst
cn.farms/vignettes/natbib.sty

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