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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
1.16.0
1.14.0
1.12.0
1.10.2
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Version
1.16.0
License
Artistic-2.0
Maintainer
Robert Scharpf
Last Published
March 5th, 2016
Functions in MinimumDistance (1.16.0)
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MDRanges-class
A
GRanges
-derived class
TrioSet-class
Deprecated class for storing low-level genomic data for trios
Defunct
Defunct functions/classes/methods in the MinimumDistance package
mad2
Deprecated wrapper for computing the median absolute deviation of low-level summaries
MinDistParam
Constructor for
MinDistParam
class
plotDenovo
Plot marker-level summaries for a genomic interval of interest
exampleTrioSetList
An example
TrioSetList
object
mindist
Getter and setter for the minimum distance statistic
mdLegend
Text summary of information encapculated in a MDRanges object for a particular interval
calculateMindist
Deprecated function to calculate the minimum distance
TrioSet
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
acf2
Function for computing autocorrelations
range,ILimit-method
compute the range of an ILimit instance
pedigreeName
Accessor for pedigree name
MinDistExperiment-class
Class and methods for MinDistExperiment
TrioSetListLD
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
coerce
Coercion methods in MinimumDistance package
pedigreeGrid
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
MAP
Computes the maximum a posteriori trio copy number state for the segmented minimum distance
Pedigree
Deprecated function for constructing an instance of class Pedigree
TrioSetList-class
Deprecated class for storing low-level genomic data for trios
md_exp
An example
MinDistExperiment
DNAcopyParam
Constructor for DNAcopyParam class
MinDistParam-class
Class and methods for parameters of minimum distance algorithm
ParentOffspringList-class
A list of
ParentOffspring
objects
MAP2
Computes maximum a posteriori estimate for the trio copy number state
PennParam
Constructor for class
PennParam
nMAD
Setter and getter for number of median absolute deviations the mean minimum distance of a genomic interval is from zero
segment2
A wrapper for DNAcopy's segment function
Pedigree-class
Deprecated class for storing pedigree data
TrioSetList
Constructor for
TrioSetList
class
filterExperiment
Methods for filtering MinDistExperiment objects
FilterParamMD
Parameters for filtering results from the segmentation and copy number inference
MinDistGRanges
Constructor for
MinDistGRanges
class
offspringNames
Deprecated functions and methods
MinDistGRanges-class
A container for storing segmentation data for members in a
ParentOffspring
family
md_gr
An example
MinDistGRanges
object
MinDistPosterior-class
Container for the segmentation results from a MinDistExperiment