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

Documentation for package ‘MinimumDistance’ version 1.53.0

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-- A --

acf2	Function for computing autocorrelations

-- C --

calculateMindist	Deprecated function to calculate the minimum distance
calculateMindist-method	Deprecated function to calculate the minimum distance
coerce	Coercion methods in MinimumDistance package
coerce-method	Deprecated class for storing low-level genomic data for trios
coerce-method	Coercion methods in MinimumDistance package

-- D --

denovo	Filter the genomic intervals for denovo copy number states
denovo-method	Filter the genomic intervals for denovo copy number states
denovoDuplication	Filter the genomic intervals for denovo copy number states
denovoDuplication-method	Filter the genomic intervals for denovo copy number states
denovoHemizygous	Filter the genomic intervals for denovo copy number states
denovoHemizygous-method	Filter the genomic intervals for denovo copy number states
denovoHomozygous	Filter the genomic intervals for denovo copy number states
denovoHomozygous-method	Filter the genomic intervals for denovo copy number states
dim-method	Deprecated class for storing pedigree data
dim-method	Deprecated class for storing low-level genomic data for trios
DNAcopyParam	Constructor for DNAcopyParam class

-- E --

exampleTrioSetList

An example 'TrioSetList' object

-- F --

father	Object containing the sample identifiers for members in a pedigree
father-method	Class and methods for MinDistExperiment
father-method	A container for storing segmentation data for members in a 'ParentOffspring' family
father-method	Object containing the sample identifiers for members in a pedigree
filterExperiment	Methods for filtering MinDistExperiment objects
filterExperiment-method	Methods for filtering MinDistExperiment objects
FilterParamMD	Parameters for filtering results from the segmentation and copy number inference
FilterParamMD-class	A class for filtering genomic intervals called by MinimumDistance

-- L --

length-method	A list of 'ParentOffspring' objects
length-method	Deprecated class for storing low-level genomic data for trios

-- M --

mad2	Deprecated wrapper for computing the median absolute deviation of low-level summaries
mad2-method	Deprecated wrapper for computing the median absolute deviation of low-level summaries
MAP	Computes the maximum a posteriori trio copy number state for the segmented minimum distance
MAP-method	Deprecated class for storing low-level genomic data for trios
MAP-method	Deprecated class for storing low-level genomic data for trios
MAP2	Computes maximum a posteriori estimate for the trio copy number state
MAP2-method	Computes maximum a posteriori estimate for the trio copy number state
mdLegend	Text summary of information encapculated in a MDRanges object for a particular interval
MDRanges	A 'GRanges'-derived class
MDRanges-class	A 'GRanges'-derived class
md_exp	An example 'MinDistExperiment'
md_gr	An example 'MinDistGRanges' object
mindist	Getter and setter for the minimum distance statistic
mindist-method	Class and methods for MinDistExperiment
mindist-method	A container for storing segmentation data for members in a 'ParentOffspring' family
mindist-method	Deprecated class for storing low-level genomic data for trios
mindist<-	Getter and setter for the minimum distance statistic
mindist<--method	Class and methods for MinDistExperiment
mindist<--method	A container for storing segmentation data for members in a 'ParentOffspring' family
mindist<--method	Deprecated class for storing low-level genomic data for trios
MinDistExperiment	Constructor for 'MinDistExperiment' class
MinDistExperiment-class	Class and methods for MinDistExperiment
MinDistExperiment-method	Constructor for 'MinDistExperiment' class
MinDistGRanges	Constructor for 'MinDistGRanges' class
MinDistGRanges-class	A container for storing segmentation data for members in a 'ParentOffspring' family
MinDistParam	Constructor for 'MinDistParam' class
MinDistParam-class	Class and methods for parameters of minimum distance algorithm
MinDistPosterior-class	Container for the segmentation results from a MinDistExperiment
MinimumDistance	De novo copy number alterations in parent-offspring trios
mother	Object containing the sample identifiers for members in a pedigree
mother-method	Class and methods for MinDistExperiment
mother-method	A container for storing segmentation data for members in a 'ParentOffspring' family
mother-method	Object containing the sample identifiers for members in a pedigree

-- N --

names-method	A container for storing segmentation data for members in a 'ParentOffspring' family
names-method	Object containing the sample identifiers for members in a pedigree
nMAD	Setter and getter for number of median absolute deviations the mean minimum distance of a genomic interval is from zero
nMAD-method	Class and methods for parameters of minimum distance algorithm
nMAD<-	Setter and getter for number of median absolute deviations the mean minimum distance of a genomic interval is from zero
nMAD<--method	Class and methods for parameters of minimum distance algorithm

-- O --

offspring	Object containing the sample identifiers for members in a pedigree
offspring-method	Class and methods for MinDistExperiment
offspring-method	A container for storing segmentation data for members in a 'ParentOffspring' family
offspring-method	Object containing the sample identifiers for members in a pedigree
offspringNames	Deprecated functions and methods
offspringNames-method	Deprecated class for storing pedigree data
offspringNames-method	Deprecated class for storing low-level genomic data for trios
offspringNames<-	Deprecated functions and methods

-- P --

ParentOffspring	Object containing the sample identifiers for members in a pedigree
ParentOffspring-class	Object containing the sample identifiers for members in a pedigree
ParentOffspringList	A list of 'ParentOffspring' objects
ParentOffspringList-class	A list of 'ParentOffspring' objects
Pedigree	Deprecated function for constructing an instance of class Pedigree
pedigree	Deprecated functions and methods
Pedigree-class	Deprecated class for storing pedigree data
pedigree-method	Class and methods for MinDistExperiment
pedigree-method	A container for storing segmentation data for members in a 'ParentOffspring' family
pedigree-method	Deprecated class for storing low-level genomic data for trios
pedigree-method	Deprecated class for storing low-level genomic data for trios
pedigree<-	Deprecated functions and methods
pedigree<--method	Class and methods for MinDistExperiment
pedigreeGrid	Plot the log R ratios and BAFs on a grid given by precomputed viewports
pedigreeName	Accessor for pedigree name
pedigreeName-method	Object containing the sample identifiers for members in a pedigree
pedigreeName-method	A list of 'ParentOffspring' objects
pedigreeViewports	Default viewports for plotting log R ratios, BAFs, chromosome idiogram, and a legend for a case-parent trio
PennParam	Constructor for class 'PennParam'
plotDenovo	Plot marker-level summaries for a genomic interval of interest
plotDenovo-method	Plot marker-level summaries for a genomic interval of interest

-- R --

range-method

compute the range of an ILimit instance

-- S --

segment2	A wrapper for DNAcopy's segment function
segment2-method	Class and methods for MinDistExperiment
segment2-method	Deprecated class for storing low-level genomic data for trios
segment2-method	A wrapper for DNAcopy's segment function
show-method	A class for filtering genomic intervals called by MinimumDistance
show-method	Class and methods for MinDistExperiment
show-method	A container for storing segmentation data for members in a 'ParentOffspring' family
show-method	Class and methods for parameters of minimum distance algorithm
show-method	Container for the segmentation results from a MinDistExperiment
show-method	Object containing the sample identifiers for members in a pedigree
show-method	A list of 'ParentOffspring' objects
show-method	Deprecated class for storing pedigree data
show-method	Constructor for class 'PennParam'
show-method	Deprecated class for storing low-level genomic data for trios
show-method	Deprecated class for storing low-level genomic data for trios
stack-method	Coercion methods in MinimumDistance package

-- T --

trios	Deprecated functions and methods
trios-method	Deprecated class for storing pedigree data
trios-method	Deprecated class for storing low-level genomic data for trios
trios-method	Deprecated class for storing low-level genomic data for trios
TrioSet	Deprecated constructor for 'TrioSet' class
TrioSet-class	Deprecated class for storing low-level genomic data for trios
TrioSetList	Constructor for 'TrioSetList' class
trioSetList	An example 'TrioSetList' object
TrioSetList-class	Deprecated class for storing low-level genomic data for trios
TrioSetListLD	Deprecated TrioSetList constructor for large data

-- misc --

"["-method	Deprecated class for storing pedigree data
"["-method	Deprecated class for storing low-level genomic data for trios
"["-method	Deprecated class for storing low-level genomic data for trios
"[["-method	A list of 'ParentOffspring' objects
"[["-method	Deprecated class for storing low-level genomic data for trios
$-method	Deprecated class for storing low-level genomic data for trios
[-method	Class and methods for MinDistExperiment
[-method	Container for the segmentation results from a MinDistExperiment
[-method	A list of 'ParentOffspring' objects
[-method	Deprecated class for storing pedigree data
[-method	Deprecated class for storing low-level genomic data for trios
[-method	Deprecated class for storing low-level genomic data for trios
[[-method	A list of 'ParentOffspring' objects
[[-method	Deprecated class for storing low-level genomic data for trios