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

Share:

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.

Author
Andreas Mitterecker, Djork-Arne Clevert
Date of publication
None
Maintainer
Andreas Mitterecker <mitterecker@bioinf.jku.at>
License
LGPL (>= 2.0)
Version
1.22.0
URLs

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