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MinimumDistance (version 1.16.0)

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

Description

Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.

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Version

Version

1.16.0

License

Artistic-2.0

Maintainer

Last Published

February 15th, 2017

Functions in MinimumDistance (1.16.0)

A GRanges-derived class

Deprecated class for storing low-level genomic data for trios

Defunct functions/classes/methods in the MinimumDistance package

Deprecated wrapper for computing the median absolute deviation of low-level summaries

Constructor for MinDistParam class

Plot marker-level summaries for a genomic interval of interest

exampleTrioSetList

An example TrioSetList object

Getter and setter for the minimum distance statistic

Text summary of information encapculated in a MDRanges object for a particular interval

calculateMindist

Deprecated function to calculate the minimum distance

Deprecated constructor for TrioSet class

ParentOffspring-class

Object containing the sample identifiers for members in a pedigree

MinimumDistance

De novo copy number alterations in parent-offspring trios

Function for computing autocorrelations

range,ILimit-method

compute the range of an ILimit instance

Accessor for pedigree name

MinDistExperiment-class

Class and methods for MinDistExperiment

Deprecated TrioSetList constructor for large data

pedigreeViewports

Default viewports for plotting log R ratios, BAFs, chromosome idiogram, and a legend for a case-parent trio

FilterParamMD-class

A class for filtering genomic intervals called by MinimumDistance

Coercion methods in MinimumDistance package

Plot the log R ratios and BAFs on a grid given by precomputed viewports

denovoHemizygous

Filter the genomic intervals for denovo copy number states

MinDistExperiment

Constructor for MinDistExperiment class

Computes the maximum a posteriori trio copy number state for the segmented minimum distance

Deprecated function for constructing an instance of class Pedigree

TrioSetList-class

Deprecated class for storing low-level genomic data for trios

An example MinDistExperiment

Constructor for DNAcopyParam class

MinDistParam-class

Class and methods for parameters of minimum distance algorithm

ParentOffspringList-class

A list of ParentOffspring objects

Computes maximum a posteriori estimate for the trio copy number state

Constructor for class PennParam

Setter and getter for number of median absolute deviations the mean minimum distance of a genomic interval is from zero

A wrapper for DNAcopy's segment function

Deprecated class for storing pedigree data

Constructor for TrioSetList class

filterExperiment

Methods for filtering MinDistExperiment objects

Parameters for filtering results from the segmentation and copy number inference

Constructor for MinDistGRanges class

Deprecated functions and methods

MinDistGRanges-class

A container for storing segmentation data for members in a ParentOffspring family

An example MinDistGRanges object

MinDistPosterior-class

Container for the segmentation results from a MinDistExperiment