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

Share:

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

Author
Robert B Scharpf and Ingo Ruczinski
Date of publication
None
Maintainer
Robert B Scharpf <rscharpf@jhu.edu>
License
Artistic-2.0
Version
1.18.0

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