Package: MinimumDistance 1.51.0
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:
MinimumDistance_1.51.0.tar.gz
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MinimumDistance.pdf |MinimumDistance.html✨
MinimumDistance/json (API)
NEWS
| # Install 'MinimumDistance' in R: |
| install.packages('MinimumDistance', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- md_exp - An example 'MinDistExperiment'
- md_gr - An example 'MinDistGRanges' object
- trioSetList - An example 'TrioSetList' object
On BioConductor:MinimumDistance-1.51.0(bioc 3.21)MinimumDistance-1.50.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraysnpcopynumbervariation
Last updated 2 months agofrom:4c9f42d26d. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 14 2024 |
| R-4.5-win | WARNING | Dec 14 2024 |
| R-4.5-linux | WARNING | Dec 14 2024 |
| R-4.4-win | WARNING | Dec 14 2024 |
| R-4.4-mac | WARNING | Dec 14 2024 |
| R-4.3-win | WARNING | Dec 14 2024 |
| R-4.3-mac | WARNING | Dec 14 2024 |
Exports:acf2calculateMindistdenovodenovoDuplicationdenovoHemizygousdenovoHomozygousDNAcopyParamfatherfilterExperimentFilterParamMDmad2MAPMAP2mdLegendMDRangesmindistmindist<-MinDistExperimentMinDistGRangesMinDistParammothernMADnMAD<-offspringoffspringNamesoffspringNames<-ParentOffspringParentOffspringListpedigreePedigreepedigree<-pedigreeGridpedigreeNamepedigreeViewportsPennParamplotDenovosegment2showstacktriosTrioSetTrioSetListTrioSetListLD
Dependencies:abindaffyioaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobBSgenomeBSgenome.Hsapiens.UCSC.hg18cachemclicodetoolscpp11crayoncrlmmcurldata.tableDBIDelayedArrayDNAcopyellipsefastmapffforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrilluminaioIRangesiteratorsjsonlitelambda.rlatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormoligoClassesopensslpkgconfigplogrpreprocessCoreR6RcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystatmodSummarizedExperimentsysUCSC.utilsVanillaICEvctrsVGAMXMLXVectoryamlzlibbioc
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 |
