Man pages for rscharpf/MinimumDistance
A Package for De Novo CNV Detection in Case-Parent Trios
| acf2 | Function for computing autocorrelations |
| calculateMindist | Deprecated function to calculate the minimum distance |
| coercion-methods | Coerces a TrioSetList to a TrioSet |
| 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 |
