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

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Functions
318
Source code
54
Man pages
44
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MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios
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API

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

Global functions
"[",Pedigree,ANY-method Man page
"[",TrioSet,ANY-method Man page
"[",TrioSetList,ANY-method Man page
"[",ff_array,ANY-method Man page
"[[",ParentOffspringList,ANY,ANY-method Man page
"[[",TrioSetList,ANY,ANY-method Man page
$,TrioSetList-method Man page
.MinDistExperiment Source code
.apply_ped_filters Source code
.calculate_mindist Source code
.checkOrder Source code
.clone_TrioSetList Source code
.constructMDE Source code
.data_frame_posteriorSummaries Source code
.dnacopy2granges Source code
.find_xlim_percent Source code
.getArm Source code
.get_md_names Source code
.initialStateProbs Source code
.mcols_posteriors Source code
.mdranges_mcols Source code
.mindist Source code
.narrowMinDistGRanges Source code
.onAttach Source code
.pedigreeId Source code
.setColnames Source code
.set_md_names Source code
.smoothAndSegment Source code
.unmake.names Source code
.validNames Source code
AssayDataList Source code
DNAcopyParam Man page Source code
Defunct Man page
FilterParamMD Man page Source code
FilterParamMD-class Man page
GenomeAnnotatedDataFrameFromList Source code
ILimit Source code
LikSet Source code
MAP Man page
MAP,TrioSet,GRanges-method Man page
MAP,TrioSetList,GRanges-method Man page
MAP2 Man page
MAP2,MinDistExperiment,GRanges-method Man page
MAP2,MinDistExperiment,GRangesList-method Man page
MAP2,MinDistExperiment,MinDistGRanges-method Man page
MDRanges Man page Source code
MDRanges-class Man page
MinDistExperiment Man page
MinDistExperiment,ArrayViews,ParentOffspring-method Man page
MinDistExperiment-class Man page
MinDistGRanges Man page Source code
MinDistGRanges-class Man page
MinDistParam Man page Source code
MinDistParam-class Man page
MinDistPosterior Source code
MinDistPosterior-class Man page
MinimumDistance Man page
ParentOffspring Man page Source code
ParentOffspring-class Man page
ParentOffspringList Man page Source code
ParentOffspringList-class Man page
Pedigree Man page Source code
Pedigree-class Man page
PennParam Man page Source code
Phi Source code
TrioSet Man page Source code
TrioSet-class Man page
TrioSetList Man page Source code
TrioSetList-class Man page
TrioSetListLD Man page Source code
[,MinDistExperiment,ANY,ANY,ANY-method Man page
[,MinDistPosterior,ANY,ANY,ANY-method Man page
[,ParentOffspringList,ANY,ANY,ANY-method Man page
[,ParentOffspringList,ANY-method Man page
[,Pedigree,ANY,ANY,ANY-method Man page
[,TrioSet,ANY,ANY,ANY-method Man page
[,TrioSetList,ANY,ANY,ANY-method Man page
[,ff_array,ANY,ANY,ANY-method Man page
[[,ParentOffspringList,ANY,ANY-method Man page
[[,TrioSetList,ANY,ANY-method Man page
acf2 Man page Source code
addRangeIndex Source code
annotatedDataFrameFromArray Source code
assayDataListDims Source code
calculateChangeSd Source code
calculateMindist Man page
calculateMindist,TrioSet-method Man page
calculateMindist,TrioSetList-method Man page
calculateMindist,arrayORff_array-method Man page
calculateMindist,list-method Man page
calculateMindist,matrix-method Man page
calculateMindistFromArray Source code
calculateMindistFromMatrix Source code
callDenovoSegments Source code
catFun2 Source code
coerce Man page
coerce,Pedigree,ParentOffspring-method Man page
coerce,RangedDataCNV,GRanges-class Man page
coerce,TrioSet,MinDistExperiment-method Man page
coerce,TrioSet,TrioSetList-method Man page
coerce,TrioSet,data.frame-method Man page
coerce,TrioSetList,MinDistExperiment-method Man page
coerce,TrioSetList,RangedSummarizedExperiment-method Man page
colAcfs Source code
combine.data.frames Source code
combineRanges Source code
combineRangesByFactor Source code
computeB Source code
computeC Source code
computeEmissionProbs Source code
concAtTop Source code
correspondingCall Source code
cumulativeLogLik Source code
dataFrameFromRange2 Source code
deletionStates Source code
denovo Man page
denovo,MinDistPosterior-method Man page
denovoDuplication Man page
denovoDuplication,MinDistPosterior-method Man page
denovoHemizygous Man page
denovoHemizygous,MinDistPosterior-method Man page
denovoHomozygous Man page
denovoHomozygous,MinDistPosterior-method Man page
dim,Pedigree-method Man page
dim,TrioSet-method Man page
discAtTop Source code
dnacopy Source code
duplicationStates Source code
duplicationStatesPenn Source code
exampleTrioSetList Man page
expandFun Source code
father Man page
father,MinDistExperiment-method Man page
father,MinDistGRanges-method Man page
father,ParentOffspring-method Man page
father,RangedSummarizedExperiment-method Man page
fillInMissing Source code
filterExperiment Man page
filterExperiment,MinDistExperiment,GRanges-method Man page
filterExperiment,MinDistExperiment,GRangesList-method Man page
filterExperiment,MinDistExperiment,MinDistGRanges-method Man page
gcSubtractMatrix Source code
generatorMatrix Source code
generatorMatrix2 Source code
generatorOverlapFeatures Source code
generatorTransitionProbs Source code
getRefGene Source code
getVarInEnv Source code
initializeLrrAndBafArrays Source code
isDeletion Source code
isDenovo Source code
isFF Source code
isLoaded Source code
length,ParentOffspringList-method Man page
length,TrioSetList-method Man page
loader Source code
logEmissionArray Source code
loglikInitial Source code
lookUpTable1 Source code
lookUpTable3 Source code
mad2 Man page
mad2,TrioSetList-method Man page
mad2,array-method Man page
mad2,list-method Man page
mad2,matrix-method Man page
madFromMatrixList Source code
madList Source code
madTrioSetList Source code
madVsCoverage Source code
make.unique2 Source code
mdLegend Man page Source code
md_exp Man page
md_gr Man page
meanLogR Source code
mindist Man page
mindist,MinDistExperiment-method Man page
mindist,MinDistGRanges-method Man page
mindist,TrioSet-method Man page
mindist<- Man page
mindist<-,MinDistExperiment,ANY-method Man page
mindist<-,MinDistGRanges,GRangesList-method Man page
mindist<-,TrioSet,matrix-method Man page
mother Man page
mother,MinDistExperiment-method Man page
mother,MinDistGRanges-method Man page
mother,ParentOffspring-method Man page
mother,RangedSummarizedExperiment-method Man page
nMAD Man page
nMAD,MinDistParam-method Man page
nMAD<- Man page
nMAD<-,MinDistParam,numeric-method Man page
names,MinDistGRanges-method Man page
names,ParentOffspring-method Man page
narrow2 Source code
narrowRangeForChromosome Source code
narrowRanges Source code
neededPkgs Source code
offspring Man page
offspring,GRangesList-method Man page
offspring,MinDistExperiment-method Man page
offspring,MinDistGRanges-method Man page
offspring,ParentOffspring-method Man page
offspring,RangedSummarizedExperiment-method Man page
offspring.hemizygous Source code
offspring.hemizygousPenn Source code
offspring.homozygous Source code
offspringIndex Source code
offspringNames Man page
offspringNames,Pedigree-method Man page
offspringNames,TrioSetList-method Man page
offspringNames<- Man page
originalNames Source code
overlapsCentromere Source code
pHet Source code
pedigree Man page
pedigree,MinDistExperiment-method Man page
pedigree,MinDistGRanges-method Man page
pedigree,TrioSet-method Man page
pedigree,TrioSetList-method Man page
pedigree<- Man page
pedigree<-,MinDistExperiment-method Man page
pedigreeGrid Man page Source code
pedigreeName Man page
pedigreeName,ParentOffspring-method Man page
pedigreeName,ParentOffspringList-method Man page
pedigreeViewports Man page Source code
phi Source code
plotDenovo Man page
plotDenovo,MinDistExperiment,MDRanges-method Man page
posterior Source code
posterior221 Source code
posteriorMAP Source code
posteriorOdds Source code
posteriorRR Source code
prTrioState Source code
pruneByFactor Source code
pruneMD Source code
pruneTrioSet Source code
range,ILimit-method Man page
read.bsfiles2 Source code
readTable1 Source code
referenceIndex Source code
removeDuplicateMapLoc Source code
rescale2 Source code
rowMAD Source code
segment2 Man page
segment2,MinDistExperiment-method Man page
segment2,TrioSet-method Man page
segment2,TrioSetList-method Man page
segment2,arrayORff_array-method Man page
segment2,ff_matrix-method Man page
segment2,list-method Man page
segment2,matrix-method Man page
segmentArray Source code
segmentList Source code
segmentMatrix Source code
segmentTrioSet Source code
segmentTrioSetList Source code
segmentff_matrix Source code
segmentff_matrix2 Source code
setSequenceLengths Source code
show,DNAcopyParam-method Man page
show,FilterParamMD-method Man page
show,MinDistExperiment-method Man page
show,MinDistGRanges-method Man page
show,MinDistParam-method Man page
show,MinDistPosterior-method Man page
show,ParentOffspring-method Man page
show,ParentOffspringList-method Man page
show,Pedigree-method Man page
show,PennParam-method Man page
show,TrioSet-method Man page
show,TrioSetList-method Man page
splitByDistance Source code
splitIndicesByLength2 Source code
stack,TrioSetLiset-method Man page
stack,TrioSetList-method Man page
stackListByColIndex Source code
stackRangedDataList Source code
stateIndex Source code
statesToEvaluate Source code
subsetGRangesById Source code
thresholdSegMeans Source code
tnorm Source code
transitionProbability Source code
trioSet2data.frame Source code
trioSetList Man page
trioSetListExample Source code
trioStateNames Source code
trioStates Source code
trios Man page
trios,Pedigree-method Man page
trios,TrioSet-method Man page
trios,TrioSetList-method Man page
unstack Source code
validAssayDataDims Source code
validPedigree Source code
vectorizeTable1 Source code
xypanelTrio Source code
xyplotTrio Source code
xyplotTrioLrrBaf Source code
yLimits Source code
MinimumDistance documentation built on Nov. 8, 2020, 11:11 p.m.

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