{ "_id": "6a0f6063acfb0bcc41c5b998", "Package": "MinimumDistance", "Title": "A Package for De Novo CNV Detection in Case-Parent Trios", "Version": "1.57.0", "Date": "2025-07-24", "Author": "Robert B Scharpf and Ingo Ruczinski", "Authors@R": "person(\"Robert\", \"Scharpf\", email=\"rscharpf@jhu.edu\", role=c(\"aut\", \"cre\"))", "Description": "Analysis of de novo copy number variants in trios from\nhigh-dimensional genotyping platforms.", "License": "Artistic-2.0", "Collate": "'help.R' 'AllClasses.R' 'AllGenerics.R' 'coercion-methods.R'\n'datasets.R' 'defunct.R' 'functions.R' 'generator-funs.R'\n'lattice-methods.R' 'mad-methods.R'\n'methods-AnnotatedDataFrame.R' 'methods-AssayData.R'\n'methods-FileViews.R' 'methods-FilterParamMD.R'\n'methods-ILimit.R' 'methods-MDRanges.R'\n'methods-MinDistExperiment.R' 'methods-MinDistGRanges.R'\n'methods-MinDistParam.R' 'methods-MinDistPosterior.R'\n'methods-ParentOffspring.R' 'methods-ParentOffspringList.R'\n'methods-Pedigree.R' 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2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 434, "source": "https://www.bioconductor.org/packages/stats/bioc/MinimumDistance" }, "_mentions": 2, "_searchresults": 10, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MinimumDistance.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_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" ], "_datasets": [ { "name": "md_exp", "title": "An example 'MinDistExperiment'", "object": "md_exp", "file": "md_exp.rda", "class": [ "MinDistExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "md_gr", "title": "An example 'MinDistGRanges' object", "object": "md_gr", "file": "md_gr.rda", "class": [ "MinDistGRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "trioSetList", "title": "An example 'TrioSetList' object", "object": "trioSetListExample", "file": "trioSetListExample.rda", "class": [ "TrioSetList" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "acf2", "title": "Function for computing autocorrelations", "topics": [ "acf2" ] }, { "page": "calculateMindist", "title": "Deprecated function to calculate the minimum distance", "topics": [ "calculateMindist", "calculateMindist,arrayORff_array-method", "calculateMindist,list-method", "calculateMindist,matrix-method", "calculateMindist,TrioSet-method", "calculateMindist,TrioSetList-method" ] }, { "page": "coercion-methods", "title": "Coercion methods in MinimumDistance package", "topics": [ "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" ] }, { "page": "denovo", "title": "Filter the genomic intervals for denovo copy number states", "topics": [ "denovo", "denovo,MinDistPosterior-method", "denovoDuplication", "denovoDuplication,MinDistPosterior-method", "denovoHemizygous", "denovoHemizygous,MinDistPosterior-method", "denovoHomozygous", "denovoHomozygous,MinDistPosterior-method" ] }, { "page": "DNAcopyParam", "title": "Constructor for DNAcopyParam class", "topics": [ "DNAcopyParam" ] }, { "page": "exampleTrioSetList", "title": "An example 'TrioSetList' object", "topics": [ "exampleTrioSetList", "trioSetList" ] }, { "page": "filterExperiment", "title": "Methods for filtering MinDistExperiment objects", "topics": [ "filterExperiment", "filterExperiment,MinDistExperiment,GRanges-method", "filterExperiment,MinDistExperiment,GRangesList-method", "filterExperiment,MinDistExperiment,MinDistGRanges-method" ] }, { "page": "FilterParamMD", "title": "Parameters for filtering results from the segmentation and copy number inference", "topics": [ "FilterParamMD" ] }, { "page": "FilterParamMD-class", "title": "A class for filtering genomic intervals called by MinimumDistance", "topics": [ "FilterParamMD-class", "show,FilterParamMD-method" ] }, { "page": "mad2", "title": "Deprecated wrapper for computing the median absolute deviation of low-level summaries", "topics": [ "mad2", "mad2,array-method", "mad2,list-method", "mad2,matrix-method", "mad2,TrioSetList-method" ] }, { "page": "MAP", "title": "Computes the maximum a posteriori trio copy number state for the segmented minimum distance", "topics": [ "MAP" ] }, { "page": "MAP2", "title": "Computes maximum a posteriori estimate for the trio copy number state", "topics": [ "MAP2", "MAP2,MinDistExperiment,GRanges-method", "MAP2,MinDistExperiment,GRangesList-method", "MAP2,MinDistExperiment,MinDistGRanges-method" ] }, { "page": "md_exp", "title": "An example 'MinDistExperiment'", "topics": [ "md_exp" ] }, { "page": "md_gr", "title": "An example 'MinDistGRanges' object", "topics": [ "md_gr" ] }, { "page": "mdLegend", "title": "Text summary of information encapculated in a MDRanges object for a particular interval", "topics": [ "mdLegend" ] }, { "page": "MDRanges-class", "title": "A 'GRanges'-derived class", "topics": [ "MDRanges", "MDRanges-class" ] }, { "page": "mindist", "title": "Getter and setter for the minimum distance statistic", "topics": [ "mindist", "mindist<-" ] }, { "page": "MinDistExperiment", "title": "Constructor for 'MinDistExperiment' class", "topics": [ "MinDistExperiment", "MinDistExperiment,ArrayViews,ParentOffspring-method" ] }, { "page": "MinDistExperiment-class", "title": "Class and methods for MinDistExperiment", "topics": [ "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" ] }, { "page": "MinDistGRanges", "title": "Constructor for 'MinDistGRanges' class", "topics": [ "MinDistGRanges" ] }, { "page": "MinDistGRanges-class", "title": "A container for storing segmentation data for members in a 'ParentOffspring' family", "topics": [ "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" ] }, { "page": "MinDistParam", "title": "Constructor for 'MinDistParam' class", "topics": [ "MinDistParam" ] }, { "page": "MinDistParam-class", "title": "Class and methods for parameters of minimum distance algorithm", "topics": [ "MinDistParam-class", "nMAD,MinDistParam-method", "nMAD<-,MinDistParam,numeric-method", "show,DNAcopyParam-method", "show,MinDistParam-method" ] }, { "page": "MinDistPosterior-class", "title": "Container for the segmentation results from a MinDistExperiment", "topics": [ "MinDistPosterior-class", "show,MinDistPosterior-method", "[,MinDistPosterior,ANY,ANY,ANY-method" ] }, { "page": "MinimumDistance", "title": "De novo copy number alterations in parent-offspring trios", "topics": [ "MinimumDistance" ] }, { "page": "nMAD", "title": "Setter and getter for number of median absolute deviations the mean minimum distance of a genomic interval is from zero", "topics": [ "nMAD", "nMAD<-" ] }, { "page": "Deprecated", "title": "Deprecated functions and methods", "topics": [ "offspringNames", "offspringNames<-", "pedigree", "pedigree<-", "trios" ] }, { "page": "ParentOffspring-class", "title": "Object containing the sample identifiers for members in a pedigree", "topics": [ "father", "father,ParentOffspring-method", "mother", "mother,ParentOffspring-method", "names,ParentOffspring-method", "offspring", "offspring,ParentOffspring-method", "ParentOffspring", "ParentOffspring-class", "pedigreeName,ParentOffspring-method", "show,ParentOffspring-method" ] }, { "page": "ParentOffspringList-class", "title": "A list of 'ParentOffspring' objects", "topics": [ "\"[[\",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" ] }, { "page": "Pedigree", "title": "Deprecated function for constructing an instance of class Pedigree", "topics": [ "Pedigree" ] }, { "page": "Pedigree-class", "title": "Deprecated class for storing pedigree data", "topics": [ "\"[\",Pedigree,ANY-method", "dim,Pedigree-method", "offspringNames,Pedigree-method", "Pedigree-class", "show,Pedigree-method", "trios,Pedigree-method", "[,Pedigree,ANY,ANY,ANY-method" ] }, { "page": "pedigreeGrid", "title": "Plot the log R ratios and BAFs on a grid given by precomputed viewports", "topics": [ "pedigreeGrid" ] }, { "page": "pedigreeName", "title": "Accessor for pedigree name", "topics": [ "pedigreeName" ] }, { "page": "pedigreeViewports", "title": "Default viewports for plotting log R ratios, BAFs, chromosome idiogram, and a legend for a case-parent trio", "topics": [ "pedigreeViewports" ] }, { "page": "PennParam", "title": "Constructor for class 'PennParam'", "topics": [ "PennParam", "show,PennParam-method" ] }, { "page": "plotDenovo", "title": "Plot marker-level summaries for a genomic interval of interest", "topics": [ "plotDenovo", "plotDenovo,MinDistExperiment,MDRanges-method" ] }, { "page": "range-ILimit-method", "title": "compute the range of an ILimit instance", "topics": [ "range,ILimit-method" ] }, { "page": "segment2", "title": "A wrapper for DNAcopy's segment function", "topics": [ "segment2", "segment2,arrayORff_array-method", "segment2,ff_matrix-method", "segment2,matrix-method", "segment2,TrioSet-method" ] }, { "page": "TrioSet", "title": "Deprecated constructor for 'TrioSet' class", "topics": [ "TrioSet" ] }, { "page": "TrioSet-class", 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