Package: MinimumDistance 1.49.0

Robert Scharpf

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.

Authors:Robert B Scharpf and Ingo Ruczinski

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MinimumDistance/json (API)
NEWS

# Install 'MinimumDistance' in R:

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

Datasets:

md_exp - An example 'MinDistExperiment'
md_gr - An example 'MinDistGRanges' object
trioSetList - An example 'TrioSetList' object

On BioConductor:MinimumDistance-1.49.0(bioc 3.20)MinimumDistance-1.48.0(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

43 exports 1.58 score 87 dependencies 2 mentions

Last updated 2 months agofrom:9a42cf5067

Exports:acf2 calculateMindist denovo denovoDuplication denovoHemizygous denovoHomozygous DNAcopyParam father filterExperiment FilterParamMD mad2 MAP MAP2 mdLegend MDRanges mindist mindist<-MinDistExperiment MinDistGRanges MinDistParam mother nMAD nMAD<-offspring offspringNames offspringNames<-ParentOffspring ParentOffspringList pedigree Pedigree pedigree<-pedigreeGrid pedigreeName pedigreeViewports PennParam plotDenovo segment2 show stack trios TrioSet TrioSetList TrioSetListLD

Dependencies:abind affyio askpass base64 beanplot BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg18 cachem cli codetools cpp11 crayon crlmm curl data.table DBI DelayedArray DNAcopy ellipse fastmap ff foreach formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges glue httr illuminaio IRanges iterators jsonlite lambda.r lattice lifecycle limma Matrix MatrixGenerics matrixStats memoise mime mvtnorm oligoClasses openssl pkgconfig plogr preprocessCore R6 Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray statmod SummarizedExperiment sys UCSC.utils VanillaICE vctrs VGAM XML XVector yaml zlibbioc

Detection of de novo copy number alterations in case-parent trios

Rendered fromMinimumDistance.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2020-10-10
Started: 2014-03-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Function for computing autocorrelations	acf2
Deprecated function to calculate the minimum distance	calculateMindist calculateMindist,arrayORff_array-method calculateMindist,list-method calculateMindist,matrix-method calculateMindist,TrioSet-method calculateMindist,TrioSetList-method
Coercion methods in MinimumDistance package	coerce coerce,Pedigree,ParentOffspring-method coerce,TrioSet,data.frame-method coerce,TrioSet,MinDistExperiment-method coerce,TrioSet,TrioSetList-method coerce,TrioSetList,MinDistExperiment-method stack,TrioSetLiset-method stack,TrioSetList-method
Filter the genomic intervals for denovo copy number states	denovo denovo,MinDistPosterior-method denovoDuplication denovoDuplication,MinDistPosterior-method denovoHemizygous denovoHemizygous,MinDistPosterior-method denovoHomozygous denovoHomozygous,MinDistPosterior-method
Constructor for DNAcopyParam class	DNAcopyParam
An example 'TrioSetList' object	exampleTrioSetList trioSetList
Methods for filtering MinDistExperiment objects	filterExperiment filterExperiment,MinDistExperiment,GRanges-method filterExperiment,MinDistExperiment,GRangesList-method filterExperiment,MinDistExperiment,MinDistGRanges-method
Parameters for filtering results from the segmentation and copy number inference	FilterParamMD
A class for filtering genomic intervals called by MinimumDistance	FilterParamMD-class show,FilterParamMD-method
Deprecated wrapper for computing the median absolute deviation of low-level summaries	mad2 mad2,array-method mad2,list-method mad2,matrix-method mad2,TrioSetList-method
Computes the maximum a posteriori trio copy number state for the segmented minimum distance	MAP
Computes maximum a posteriori estimate for the trio copy number state	MAP2 MAP2,MinDistExperiment,GRanges-method MAP2,MinDistExperiment,GRangesList-method MAP2,MinDistExperiment,MinDistGRanges-method
An example 'MinDistExperiment'	md_exp
An example 'MinDistGRanges' object	md_gr
Text summary of information encapculated in a MDRanges object for a particular interval	mdLegend
A 'GRanges'-derived class	MDRanges MDRanges-class
Getter and setter for the minimum distance statistic	mindist mindist<-
Constructor for 'MinDistExperiment' class	MinDistExperiment MinDistExperiment,ArrayViews,ParentOffspring-method
Class and methods for MinDistExperiment	father,MinDistExperiment-method father,RangedSummarizedExperiment-method mindist,MinDistExperiment-method mindist<-,MinDistExperiment,ANY-method MinDistExperiment-class mother,MinDistExperiment-method mother,RangedSummarizedExperiment-method offspring,MinDistExperiment-method offspring,RangedSummarizedExperiment-method pedigree,MinDistExperiment-method pedigree<-,MinDistExperiment-method segment2,MinDistExperiment-method show,MinDistExperiment-method [,MinDistExperiment,ANY,ANY,ANY-method
Constructor for 'MinDistGRanges' class	MinDistGRanges
A container for storing segmentation data for members in a 'ParentOffspring' family	father,MinDistGRanges-method mindist,MinDistGRanges-method mindist<-,MinDistGRanges,GRangesList-method MinDistGRanges-class mother,MinDistGRanges-method names,MinDistGRanges-method offspring,GRangesList-method offspring,MinDistGRanges-method pedigree,MinDistGRanges-method show,MinDistGRanges-method
Constructor for 'MinDistParam' class	MinDistParam
Class and methods for parameters of minimum distance algorithm	MinDistParam-class nMAD,MinDistParam-method nMAD<-,MinDistParam,numeric-method show,DNAcopyParam-method show,MinDistParam-method
Container for the segmentation results from a MinDistExperiment	MinDistPosterior-class show,MinDistPosterior-method [,MinDistPosterior,ANY,ANY,ANY-method
De novo copy number alterations in parent-offspring trios	MinimumDistance
Setter and getter for number of median absolute deviations the mean minimum distance of a genomic interval is from zero	nMAD nMAD<-
Deprecated functions and methods	offspringNames offspringNames<- pedigree pedigree<- trios
Object containing the sample identifiers for members in a pedigree	father father,ParentOffspring-method mother mother,ParentOffspring-method names,ParentOffspring-method offspring offspring,ParentOffspring-method ParentOffspring ParentOffspring-class pedigreeName,ParentOffspring-method show,ParentOffspring-method
A list of 'ParentOffspring' objects	"[[",ParentOffspringList,ANY,ANY-method length,ParentOffspringList-method ParentOffspringList ParentOffspringList-class pedigreeName,ParentOffspringList-method show,ParentOffspringList-method [,ParentOffspringList,ANY,ANY,ANY-method [,ParentOffspringList,ANY-method [[,ParentOffspringList,ANY,ANY-method
Deprecated function for constructing an instance of class Pedigree	Pedigree
Deprecated class for storing pedigree data	"[",Pedigree,ANY-method dim,Pedigree-method offspringNames,Pedigree-method Pedigree-class show,Pedigree-method trios,Pedigree-method [,Pedigree,ANY,ANY,ANY-method
Plot the log R ratios and BAFs on a grid given by precomputed viewports	pedigreeGrid
Accessor for pedigree name	pedigreeName
Default viewports for plotting log R ratios, BAFs, chromosome idiogram, and a legend for a case-parent trio	pedigreeViewports
Constructor for class 'PennParam'	PennParam show,PennParam-method
Plot marker-level summaries for a genomic interval of interest	plotDenovo plotDenovo,MinDistExperiment,MDRanges-method
compute the range of an ILimit instance	range,ILimit-method
A wrapper for DNAcopy's segment function	segment2 segment2,arrayORff_array-method segment2,ff_matrix-method segment2,matrix-method segment2,TrioSet-method
Deprecated constructor for 'TrioSet' class	TrioSet
Deprecated class for storing low-level genomic data for trios	"[",ff_array,ANY-method "[",TrioSet,ANY-method dim,TrioSet-method MAP,TrioSet,GRanges-method mindist,TrioSet-method mindist<-,TrioSet,matrix-method pedigree,TrioSet-method show,TrioSet-method trios,TrioSet-method TrioSet-class [,ff_array,ANY,ANY,ANY-method [,TrioSet,ANY,ANY,ANY-method
Constructor for 'TrioSetList' class	TrioSetList
Deprecated class for storing low-level genomic data for trios	"[",TrioSetList,ANY-method "[[",TrioSetList,ANY,ANY-method $,TrioSetList-method coerce,TrioSetList,RangedSummarizedExperiment-method length,TrioSetList-method MAP,TrioSetList,GRanges-method offspringNames,TrioSetList-method pedigree,TrioSetList-method segment2,list-method segment2,TrioSetList-method show,TrioSetList-method trios,TrioSetList-method TrioSetList-class [,TrioSetList,ANY,ANY,ANY-method [[,TrioSetList,ANY,ANY-method
Deprecated TrioSetList constructor for large data	TrioSetListLD