Package: cn.farms 1.53.0

Andreas Mitterecker

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.

Authors:Andreas Mitterecker, Djork-Arne Clevert

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cn.farms.pdf |cn.farms.html✨
cn.farms/json (API)

# Install 'cn.farms' in R:

install.packages('cn.farms', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:cn.farms-1.53.0(bioc 3.20)cn.farms-1.52.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

31 exports 1.08 score 57 dependencies

Last updated 2 months agofrom:c0d7cd9f49

Exports:cn.farms cnLibrary combineData createAnnotation createMatrix distributionDistance dnaCopySf fragLengCorr mlSummarization normalizeAverage normalizeCels normalizeNpData normalizeSequenceEffect plotDendrogram plotDensity plotEvalIc plotRegions plotSmoothScatter plotViolines slSummarization sparseFarmsC summarizeFarmsExact summarizeFarmsExact2 summarizeFarmsExact3 summarizeFarmsGaussian summarizeFarmsMethods summarizeFarmsStatistics summarizeFarmsVariational summarizeWindowBps summarizeWindowMethods summarizeWindowStd

Dependencies:abind affxparser affyio askpass Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI DelayedArray DNAcopy fastmap ff foreach GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges iterators jsonlite lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime oligo oligoClasses openssl pkgconfig plogr preprocessCore R6 rlang RSQLite S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils vctrs XVector zlibbioc

cn.farms: Manual for the R package

Rendered fromcn.farms.Rnwusingutils::Sweaveon Jul 07 2024.

Last update: 2014-05-16
Started: 2012-11-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Defines which variables should be written back when calling a cn.farms run	callSummarize
cn.farms	cn.farms
This function was taken from snowfall and edited due to some deprecated function calls.	cnLibrary
Combine two ExpressionSet objects	combineData
Creation of annotation files	createAnnotation
Creates the needed matrix	createMatrix
Computes the distribution distance	distributionDistance
Runs DNAcopy in parallel mode	dnaCopySf
Does the whole cn.farms process in one call	doCnFarmsSingle
Does a fragment length correction on intensities	flcSnp6Std
Does a fragment length correction on intensities	flcStd
Does a fragment length correction	fragLengCorr
Finds SNPs which belong to one fragment	getFragmentSet
Combines data for probeset summarization	getSingleProbeSetSize
Method for computation of the multi-loci summarization	mlSummarization
Extracts info from the package name	normAdd
Scales the range of the non-polymorphic data to the range of a given array.	normalizeAverage
Wrapper for the normalization functions	normalizeCels
Runs the SOR normalization on microarray data	normalizeNone
Processes the non-polymorphic data	normalizeNpData
Normalization Quantiles	normalizeQuantiles
Correction for probe sequence effects	normalizeSequenceEffect
Runs the SOR normalization on microarray data	normalizeSor
Plots a dendrogram	plotDendrogram
Function to create a density plot	plotDensity
Creates a plot with known regions and a numeric vector	plotEvalIc
Plots given regions by segments	plotRegions
Creates a smooth scatter plot	plotSmoothScatter
Create a violine plot	plotViolines
Method for computation of the single-locus summarization	slSummarization
Normalizes the data with SOR	sparseFarmsC
Summarization Laplacian approach with exact computation	summarizeFarmsExact
Summarization Laplacian approach with exact computation	summarizeFarmsExact2
Summarization Laplacian approach with exact computation	summarizeFarmsExact3
Summarization Gaussian approach	summarizeFarmsGaussian
Lists methods for possible FARMS summarization	summarizeFarmsMethods
Mean or median instead of the FARMS model	summarizeFarmsStatistics
Summarization variational Laplacian approach	summarizeFarmsVariational
Combines neighbouring locations to windows	summarizeWindowBps
Lists methods for possible window methods	summarizeWindowMethods
Combines neighbouring locations to windows	summarizeWindowStd