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

Functions

callSummarize Man page
cn.farms Man page
cnLibrary Man page
combineData Man page
createAnnotation Man page
createMatrix Man page
distributionDistance Man page
dnaCopySf Man page
doCnFarmsSingle Man page
flcSnp6Std Man page
flcStd Man page
fragLengCorr Man page
getFragmentSet Man page
getSingleProbeSetSize Man page
mlSummarization Man page
normAdd Man page
normalizeAverage Man page
normalizeCels Man page
normalizeNone Man page
normalizeNpData Man page
normalizeQuantiles Man page
normalizeSequenceEffect Man page
normalizeSor Man page
plotDendrogram Man page
plotDensity Man page
plotEvalIc Man page
plotRegions Man page
plotSmoothScatter Man page
plotViolines Man page
slSummarization Man page
sparseFarmsC Man page
summarizeFarmsExact Man page
summarizeFarmsExact2 Man page
summarizeFarmsExact3 Man page
summarizeFarmsGaussian Man page
summarizeFarmsMethods Man page
summarizeFarmsStatistics Man page
summarizeFarmsVariational Man page
summarizeWindowBps Man page
summarizeWindowMethods Man page
summarizeWindowStd Man page

Files

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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