A B C D F G I L M N O P S T U X misc
allNames | Class '"TrioSetList"' |
allNames-method | Container for storing pedigree information |
allNames-method | Class '"TrioSet"' |
allNames-method | Class '"TrioSetList"' |
annotatedDataFrameFrom-method | Methods for creating AnnotatedDataFrame objects |
annotatedDataFrameFrom-methods | Methods for creating AnnotatedDataFrame objects |
annotation-method | Class '"TrioSetList"' |
baf | Class '"TrioSetList"' |
baf-method | Class '"TrioSet"' |
baf-method | Class '"TrioSetList"' |
baf<- | Class '"TrioSet"' |
baf<--method | Class '"TrioSet"' |
calculateMindist | Compute the minimum distance. |
calculateMindist-method | Class '"TrioSet"' |
calculateMindist-method | Compute the minimum distance. |
callDenovoSegments | Posterior calling for segmented data. |
coerce-method | Class '"TrioSet"' |
coerce-method | Methods for coercing objects from one class to another |
computeBayesFactor | Compute Bayes factors for minimum distance segments |
computeBayesFactor-method | Class '"TrioSet"' |
computeBayesFactor-method | Class '"TrioSetList"' |
concAtTop | Functions for assessing concordance |
correspondingCall | Find overlapping ranges |
dim-method | Container for storing pedigree information |
dim-method | Class '"TrioSet"' |
dims-method | Class '"TrioSetList"' |
discAtTop | Functions for assessing concordance |
fatherNames | Class '"TrioSetList"' |
fatherNames-method | Container for storing pedigree information |
fatherNames-method | Class '"TrioSet"' |
fatherNames-method | Class '"TrioSetList"' |
fatherNames<- | Class '"TrioSet"' |
fatherNames<--method | Class '"TrioSet"' |
fatherPhenoData | Extract phenotype data for parents in a trio. |
fatherPhenoData-method | Class '"TrioSet"' |
fatherPhenoData-method | Class '"TrioSetList"' |
featureData-method | Class '"TrioSetList"' |
gcSubtract | Generic function for GC correction |
gcSubtract-method | Class '"TrioSet"' |
gcSubtract-method | Class '"TrioSetList"' |
initialize-method | Container for storing pedigree information |
initialize-method | Class '"TrioSet"' |
initialize-method | Class '"TrioSetList"' |
isDenovo | Indicator for whether a trio copy number state is a de novo copy number alteration. |
length-method | Class '"TrioSetList"' |
lrr-method | Class '"TrioSet"' |
lrr-method | Class '"TrioSetList"' |
lrr.segs | Objects containing segmented data |
lrr<- | Class '"TrioSet"' |
lrr<--method | Class '"TrioSet"' |
mad2 | Methods for computing the minimum absolute distance. |
mad2-method | Class '"TrioSetList"' |
mad2-method | Methods for computing the minimum absolute distance. |
map.segs | Objects containing segmented data |
md.segs | Objects containing segmented data |
mindist | Class '"TrioSet"' |
mindist-method | Class '"TrioSet"' |
mindist-method | Class '"TrioSetList"' |
mindist<- | Class '"TrioSet"' |
mindist<--method | Class '"TrioSet"' |
mindist<--method | Class '"TrioSetList"' |
motherNames | Class '"TrioSetList"' |
motherNames-method | Container for storing pedigree information |
motherNames-method | Class '"TrioSet"' |
motherNames-method | Class '"TrioSetList"' |
motherPhenoData | Extract phenotype data for parents in a trio. |
motherPhenoData-method | Class '"TrioSet"' |
motherPhenoData-method | Class '"TrioSetList"' |
narrow | Adjust breakpoints from segmentation inward |
ncol-method | Class '"TrioSet"' |
ncol-method | Class '"TrioSetList"' |
nrow-method | Class '"TrioSetList"' |
offspringNames | Class '"TrioSetList"' |
offspringNames-method | Container for storing pedigree information |
offspringNames-method | Class '"TrioSet"' |
offspringNames-method | Class '"TrioSetList"' |
offspringPhenoData | Class '"TrioSet"' |
offspringPhenoData-method | Class '"TrioSet"' |
offspringPhenoData-method | Class '"TrioSetList"' |
order-method | Class '"TrioSet"' |
order-method | Class '"TrioSetList"' |
Pedigree | Constructor for Pedigree class |
pedigree | Class '"TrioSetList"' |
Pedigree-class | Container for storing pedigree information |
pedigree-method | Class '"TrioSet"' |
pedigree-method | Class '"TrioSetList"' |
phenoData-method | Class '"TrioSetList"' |
sampleNames-method | Class '"TrioSetList"' |
segment2 | Wrapper for segment function in package DNAcopy |
segment2-method | Wrapper for segment function in package DNAcopy |
stack-method | Class '"TrioSetList"' |
stackRangedDataList | Stack a list of RangedDataCBS objects. |
trios | Class '"TrioSetList"' |
trios-method | Container for storing pedigree information |
trios-method | Class '"TrioSet"' |
trios-method | Class '"TrioSetList"' |
TrioSet | Constructor for TrioSet objects. |
TrioSet-class | Class '"TrioSet"' |
TrioSetList | Constructs and object of class 'TrioSetList' |
trioSetList | An example of a 'TrioSetList' object |
TrioSetList-class | Class '"TrioSetList"' |
trioSetListExample | An example of a 'TrioSetList' object |
TrioSetListLD | Constructor for TrioSetList class for large data |
updateObject-method | Class '"TrioSet"' |
updateObject-method | Class '"TrioSetList"' |
xypanelTrio | Panel function for a lattice-style plot of log R ratios, BAFs, and the minimum distance for a trio. |
xyplot-method | Class '"TrioSet"' |
xyplotTrio | Function for plotting log R ratios, BAFs, and the minimum distance for a trio using lattice. |
$-method | Class '"TrioSetList"' |
[-method | Container for storing pedigree information |
[-method | Class '"TrioSet"' |
[-method | Class '"TrioSetList"' |
[[-method | Class '"TrioSetList"' |