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 |
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 |
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 |
"["-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 |