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 |
acf2 | Function for computing autocorrelations |
as | Coercion methods in MinimumDistance package |
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 |
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 |
exampleTrioSetList | An example 'TrioSetList' object |
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 |
length-method | A list of 'ParentOffspring' objects |
length-method | Deprecated class for storing low-level genomic data for trios |
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 |
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 |
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 |
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 |
range-method | compute the range of an ILimit instance |
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 |
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 |