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

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**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**Browse all...**

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