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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MinimumDistance")
AuthorRobert B Scharpf and Ingo Ruczinski
Bioconductor views CopyNumberVariation Microarray SNP
Date of publicationNone
MaintainerRobert B Scharpf <rscharpf@jhu.edu>
LicenseArtistic-2.0
Version1.20.0

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

Functions

acf2 Man page
as Man page
calculateMindist Man page
calculateMindist,arrayORff_array-method Man page
calculateMindist,list-method Man page
calculateMindist,matrix-method Man page
calculateMindist,TrioSetList-method Man page
calculateMindist,TrioSet-method Man page
coerce Man page
coerce,Pedigree,ParentOffspring-method Man page
coerce,RangedDataCNV,GRanges-class Man page
coerce,TrioSet,data.frame-method Man page
coerce,TrioSetList,MinDistExperiment-method Man page
coerce,TrioSetList,RangedSummarizedExperiment-method Man page
coerce,TrioSet,MinDistExperiment-method Man page
coerce,TrioSet,TrioSetList-method Man page
Defunct Man page
denovo Man page
denovoDuplication Man page
denovoDuplication,MinDistPosterior-method Man page
denovoHemizygous Man page
denovoHemizygous,MinDistPosterior-method Man page
denovoHomozygous Man page
denovoHomozygous,MinDistPosterior-method Man page
denovo,MinDistPosterior-method Man page
dim,Pedigree-method Man page
dim,TrioSet-method Man page
DNAcopyParam Man page
exampleTrioSetList Man page
father Man page
father,MinDistExperiment-method Man page
father,MinDistGRanges-method Man page
father,ParentOffspring-method Man page
father,RangedSummarizedExperiment-method Man page
[,ff_array,ANY,ANY,ANY-method Man page
"[",ff_array,ANY-method Man page
filterExperiment Man page
filterExperiment,MinDistExperiment,GRangesList-method Man page
filterExperiment,MinDistExperiment,GRanges-method Man page
filterExperiment,MinDistExperiment,MinDistGRanges-method Man page
FilterParamMD Man page
FilterParamMD-class Man page
length,ParentOffspringList-method Man page
length,TrioSetList-method Man page
mad2 Man page
mad2,array-method Man page
mad2,list-method Man page
mad2,matrix-method Man page
mad2,TrioSetList-method Man page
MAP Man page
MAP2 Man page
MAP2,MinDistExperiment,GRangesList-method Man page
MAP2,MinDistExperiment,GRanges-method Man page
MAP2,MinDistExperiment,MinDistGRanges-method Man page
MAP,TrioSet,GRanges-method Man page
MAP,TrioSetList,GRanges-method Man page
md_exp Man page
md_gr Man page
mdLegend Man page
MDRanges Man page
MDRanges-class Man page
mindist Man page
mindist<- Man page
MinDistExperiment Man page
[,MinDistExperiment,ANY,ANY,ANY-method Man page
MinDistExperiment,ArrayViews,ParentOffspring-method Man page
MinDistExperiment-class Man page
MinDistGRanges Man page
MinDistGRanges-class Man page
mindist<-,MinDistExperiment,ANY-method Man page
mindist,MinDistExperiment-method Man page
mindist<-,MinDistGRanges,GRangesList-method Man page
mindist,MinDistGRanges-method Man page
MinDistParam Man page
MinDistParam-class Man page
[,MinDistPosterior,ANY,ANY,ANY-method Man page
MinDistPosterior-class Man page
mindist<-,TrioSet,matrix-method Man page
mindist,TrioSet-method Man page
MinimumDistance Man page
MinimumDistance-package Man page
mother Man page
mother,MinDistExperiment-method Man page
mother,MinDistGRanges-method Man page
mother,ParentOffspring-method Man page
mother,RangedSummarizedExperiment-method Man page
names,MinDistGRanges-method Man page
names,ParentOffspring-method Man page
nMAD Man page
nMAD<- Man page
nMAD,MinDistParam-method Man page
nMAD<-,MinDistParam,numeric-method Man page
offspring Man page
offspring,GRangesList-method Man page
offspring,MinDistExperiment-method Man page
offspring,MinDistGRanges-method Man page
offspringNames Man page
offspringNames<- Man page
offspringNames,Pedigree-method Man page
offspringNames,TrioSetList-method Man page
offspring,ParentOffspring-method Man page
offspring,RangedSummarizedExperiment-method Man page
ParentOffspring Man page
ParentOffspring-class Man page
ParentOffspringList Man page
[,ParentOffspringList,ANY,ANY,ANY-method Man page
"[[",ParentOffspringList,ANY,ANY-method Man page
[[,ParentOffspringList,ANY,ANY-method Man page
[,ParentOffspringList,ANY-method Man page
ParentOffspringList-class Man page
pedigree Man page
pedigree<- Man page
Pedigree Man page
[,Pedigree,ANY,ANY,ANY-method Man page
"[",Pedigree,ANY-method Man page
Pedigree-class Man page
pedigreeGrid Man page
pedigree<-,MinDistExperiment-method Man page
pedigree,MinDistExperiment-method Man page
pedigree,MinDistGRanges-method Man page
pedigreeName Man page
pedigreeName,ParentOffspringList-method Man page
pedigreeName,ParentOffspring-method Man page
pedigree,TrioSetList-method Man page
pedigree,TrioSet-method Man page
pedigreeViewports Man page
PennParam Man page
plotDenovo Man page
plotDenovo,MinDistExperiment,MDRanges-method Man page
range,ILimit-method Man page
segment2 Man page
segment2,arrayORff_array-method Man page
segment2,ff_matrix-method Man page
segment2,list-method Man page
segment2,matrix-method Man page
segment2,MinDistExperiment-method Man page
segment2,TrioSetList-method Man page
segment2,TrioSet-method Man page
show,DNAcopyParam-method Man page
show,FilterParamMD-method Man page
show,MinDistExperiment-method Man page
show,MinDistGRanges-method Man page
show,MinDistParam-method Man page
show,MinDistPosterior-method Man page
show,ParentOffspringList-method Man page
show,ParentOffspring-method Man page
show,Pedigree-method Man page
show,PennParam-method Man page
show,TrioSetList-method Man page
show,TrioSet-method Man page
stack,TrioSetLiset-method Man page
stack,TrioSetList-method Man page
trios Man page
TrioSet Man page
[,TrioSet,ANY,ANY,ANY-method Man page
"[",TrioSet,ANY-method Man page
TrioSet-class Man page
trioSetList Man page
TrioSetList Man page
[,TrioSetList,ANY,ANY,ANY-method Man page
"[[",TrioSetList,ANY,ANY-method Man page
[[,TrioSetList,ANY,ANY-method Man page
"[",TrioSetList,ANY-method Man page
TrioSetList-class Man page
TrioSetListLD Man page
$,TrioSetList-method Man page
trios,Pedigree-method Man page
trios,TrioSetList-method Man page
trios,TrioSet-method Man page

Files

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

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