MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.

AuthorRobert B Scharpf and Ingo Ruczinski
Date of publicationNone
MaintainerRobert B Scharpf <rscharpf@jhu.edu>
LicenseArtistic-2.0
Version1.18.0

View on Bioconductor

Man pages

acf2: Function for computing autocorrelations

calculateMindist: Deprecated function to calculate the minimum distance

coercion-methods: Coercion methods in MinimumDistance package

Defunct: Defunct functions/classes/methods in the MinimumDistance...

denovo: Filter the genomic intervals for denovo copy number states

Deprecated: Deprecated functions and methods

DNAcopyParam: Constructor for DNAcopyParam class

exampleTrioSetList: An example 'TrioSetList' object

filterExperiment: Methods for filtering MinDistExperiment objects

FilterParamMD: Parameters for filtering results from the segmentation and...

FilterParamMD-class: A class for filtering genomic intervals called by...

mad2: Deprecated wrapper for computing the median absolute...

MAP: Computes the maximum a posteriori trio copy number state for...

MAP2: Computes maximum a posteriori estimate for the trio copy...

md_exp: An example 'MinDistExperiment'

md_gr: An example 'MinDistGRanges' object

mdLegend: Text summary of information encapculated in a MDRanges object...

MDRanges-class: A 'GRanges'-derived class

mindist: Getter and setter for the minimum distance statistic

MinDistExperiment: Constructor for 'MinDistExperiment' class

MinDistExperiment-class: Class and methods for MinDistExperiment

MinDistGRanges: Constructor for 'MinDistGRanges' class

MinDistGRanges-class: A container for storing segmentation data for members in a...

MinDistParam: Constructor for 'MinDistParam' class

MinDistParam-class: Class and methods for parameters of minimum distance...

MinDistPosterior-class: Container for the segmentation results from a...

MinimumDistance: De novo copy number alterations in parent-offspring trios

nMAD: Setter and getter for number of median absolute deviations...

ParentOffspring-class: Object containing the sample identifiers for members in a...

ParentOffspringList-class: A list of 'ParentOffspring' objects

Pedigree: Deprecated function for constructing an instance of class...

Pedigree-class: Deprecated class for storing pedigree data

pedigreeGrid: Plot the log R ratios and BAFs on a grid given by precomputed...

pedigreeName: Accessor for pedigree name

pedigreeViewports: Default viewports for plotting log R ratios, BAFs, chromosome...

PennParam: Constructor for class 'PennParam'

plotDenovo: Plot marker-level summaries for a genomic interval of...

range-ILimit-method: compute the range of an ILimit instance

segment2: A wrapper for DNAcopy's segment function

TrioSet: Deprecated constructor for 'TrioSet' class

TrioSet-class: Deprecated class for storing low-level genomic data for trios

TrioSetList: Constructor for 'TrioSetList' class

TrioSetList-class: Deprecated class for storing low-level genomic data for trios

TrioSetListLD: Deprecated TrioSetList constructor for large data

Files in this package

MinimumDistance/DESCRIPTION
MinimumDistance/NAMESPACE
MinimumDistance/NEWS
MinimumDistance/R
MinimumDistance/R/AllClasses.R MinimumDistance/R/AllGenerics.R MinimumDistance/R/coercion-methods.R MinimumDistance/R/datasets.R MinimumDistance/R/defunct.R MinimumDistance/R/functions.R MinimumDistance/R/generator-funs.R MinimumDistance/R/help.R MinimumDistance/R/lattice-methods.R MinimumDistance/R/mad-methods.R MinimumDistance/R/methods-AnnotatedDataFrame.R MinimumDistance/R/methods-AssayData.R MinimumDistance/R/methods-FileViews.R MinimumDistance/R/methods-FilterParamMD.R MinimumDistance/R/methods-ILimit.R MinimumDistance/R/methods-MDRanges.R MinimumDistance/R/methods-MinDistExperiment.R MinimumDistance/R/methods-MinDistGRanges.R MinimumDistance/R/methods-MinDistParam.R MinimumDistance/R/methods-MinDistPosterior.R MinimumDistance/R/methods-ParentOffspring.R MinimumDistance/R/methods-ParentOffspringList.R MinimumDistance/R/methods-Pedigree.R MinimumDistance/R/methods-PennParam.R MinimumDistance/R/methods-ShallowSimpleList.R MinimumDistance/R/methods-SummarizedExperiment.R MinimumDistance/R/methods-TrioSet.R MinimumDistance/R/methods-TrioSetList.R MinimumDistance/R/methods-ff_array.R MinimumDistance/R/methods-grid.R MinimumDistance/R/methods-list.R MinimumDistance/R/methods-matrix.R MinimumDistance/R/segment2-methods.R MinimumDistance/R/utils.R MinimumDistance/R/zzz.R
MinimumDistance/build
MinimumDistance/build/vignette.rds
MinimumDistance/data
MinimumDistance/data/md_exp.rda
MinimumDistance/data/md_gr.rda
MinimumDistance/data/trioSetListExample.rda
MinimumDistance/inst
MinimumDistance/inst/NEWS.Rd
MinimumDistance/inst/doc
MinimumDistance/inst/doc/MinimumDistance.R
MinimumDistance/inst/doc/MinimumDistance.Rnw
MinimumDistance/inst/doc/MinimumDistance.pdf
MinimumDistance/inst/extdata
MinimumDistance/inst/extdata/F.txt
MinimumDistance/inst/extdata/M.txt
MinimumDistance/inst/extdata/O.txt
MinimumDistance/inst/extdata/O1.txt
MinimumDistance/inst/extdata/baf.rda
MinimumDistance/inst/extdata/exampleFiles.R
MinimumDistance/inst/extdata/logRratio.rda
MinimumDistance/inst/extdata/md_granges.rds
MinimumDistance/inst/extdata/mdgr.rds
MinimumDistance/inst/extdata/pedigreeInfo.rda
MinimumDistance/inst/extdata/pennCNV_MendelianProb.rda
MinimumDistance/inst/extdata/sample.sheet.rda
MinimumDistance/inst/extdata/trioSet12023chr12.rda
MinimumDistance/inst/scripts
MinimumDistance/inst/scripts/Affy2.R
MinimumDistance/inst/scripts/Discordance.Rnw
MinimumDistance/inst/scripts/Sweave.sty
MinimumDistance/inst/scripts/affy.R
MinimumDistance/inst/scripts/cleft_notParallel.Rnw
MinimumDistance/inst/scripts/logR.baf.rda
MinimumDistance/inst/scripts/runDiscordance.R
MinimumDistance/inst/unitTests
MinimumDistance/inst/unitTests/Makefile
MinimumDistance/inst/unitTests/test_FilterParam.R
MinimumDistance/inst/unitTests/test_MinDistExperiment.R
MinimumDistance/inst/unitTests/test_Pedigree-class.R
MinimumDistance/inst/unitTests/test_PedigreeViews.R
MinimumDistance/inst/unitTests/test_SnpArrayExperiment.R
MinimumDistance/inst/unitTests/test_TrioSetList.R
MinimumDistance/inst/unitTests/test_calculateMindist.R
MinimumDistance/inst/unitTests/test_callDenovoSegments.R
MinimumDistance/inst/unitTests/test_few_markers.R
MinimumDistance/inst/unitTests/test_posteriorCalls.R
MinimumDistance/inst/unitTests/test_quads.R
MinimumDistance/inst/unitTests/test_rdsViews.R
MinimumDistance/inst/unitTests/test_splitsForCBS.R
MinimumDistance/man
MinimumDistance/man/DNAcopyParam.Rd MinimumDistance/man/Defunct.Rd MinimumDistance/man/Deprecated.Rd MinimumDistance/man/FilterParamMD-class.Rd MinimumDistance/man/FilterParamMD.Rd MinimumDistance/man/MAP.Rd MinimumDistance/man/MAP2.Rd MinimumDistance/man/MDRanges-class.Rd MinimumDistance/man/MinDistExperiment-class.Rd MinimumDistance/man/MinDistExperiment.Rd MinimumDistance/man/MinDistGRanges-class.Rd MinimumDistance/man/MinDistGRanges.Rd MinimumDistance/man/MinDistParam-class.Rd MinimumDistance/man/MinDistParam.Rd MinimumDistance/man/MinDistPosterior-class.Rd MinimumDistance/man/MinimumDistance.Rd MinimumDistance/man/ParentOffspring-class.Rd MinimumDistance/man/ParentOffspringList-class.Rd MinimumDistance/man/Pedigree-class.Rd MinimumDistance/man/Pedigree.Rd MinimumDistance/man/PennParam.Rd MinimumDistance/man/TrioSet-class.Rd MinimumDistance/man/TrioSet.Rd MinimumDistance/man/TrioSetList-class.Rd MinimumDistance/man/TrioSetList.Rd MinimumDistance/man/TrioSetListLD.Rd MinimumDistance/man/acf2.Rd MinimumDistance/man/calculateMindist.Rd MinimumDistance/man/coercion-methods.Rd MinimumDistance/man/denovo.Rd MinimumDistance/man/exampleTrioSetList.Rd MinimumDistance/man/filterExperiment.Rd MinimumDistance/man/mad2.Rd MinimumDistance/man/mdLegend.Rd MinimumDistance/man/md_exp.Rd MinimumDistance/man/md_gr.Rd MinimumDistance/man/mindist.Rd MinimumDistance/man/nMAD.Rd MinimumDistance/man/pedigreeGrid.Rd MinimumDistance/man/pedigreeName.Rd MinimumDistance/man/pedigreeViewports.Rd MinimumDistance/man/plotDenovo.Rd MinimumDistance/man/range-ILimit-method.Rd MinimumDistance/man/segment2.Rd
MinimumDistance/tests
MinimumDistance/tests/doRUnit.R
MinimumDistance/vignettes
MinimumDistance/vignettes/MinimumDistance.Rnw
MinimumDistance/vignettes/MinimumDistance.bib

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