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

## Documentation for package ‘MinimumDistance’ version 1.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

## -- C --

calculateMindist | Deprecated function to calculate the minimum distance
calculateMindist-method | Deprecated function to calculate the minimum distance
coerce | Coerces a TrioSetList to a TrioSet
coerce-method | Deprecated class for storing low-level genomic data for trios
coerce-method | Coerces a TrioSetList to a TrioSet

## -- 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 | Coerces a TrioSetList to a TrioSet

## -- 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