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

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Documentation for package ‘MinimumDistance’ version 1.22.0

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A C D E F L M N O P R S T misc

MinimumDistance-package De novo copy number alterations in parent-offspring trios

-- A --

acf2 Function for computing autocorrelations
as Coercion methods in MinimumDistance package

-- 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