Index

A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W | Z

A

activateByChromosome() (in module spreadsheet)
activeSubset() (in module spreadsheet)
addBoolColumn() (in module datasetbuilder)
addCategoricalColumn() (in module datasetbuilder)
addColumn() (in module datasetbuilder)
addCommonName() (in module genomemap)
addGeneticColumn() (in module datasetbuilder)
addGenotypicColumn() (in module datasetbuilder)
addHeader() (in module resultviewer)
addIntColumn() (in module datasetbuilder)
addIntegerColumn() (in module datasetbuilder)
addIntField() (in module markermapbuilderbyfield)
addList() (in module resultviewer)
addMapIntField() (in module datasetbuilder)
addMapRealField() (in module datasetbuilder)
addMapStringField() (in module datasetbuilder)
addMarker() (in module markermapbuilderbymarker)
addMarkerMap() (in module datasetbuilder)
addPairedList() (in module resultviewer)
addRealColumn() (in module datasetbuilder)
addRealField() (in module markermapbuilderbyfield)
addRowLabels() (in module datasetbuilder)
addStringField() (in module markermapbuilderbyfield)
addSubHeader() (in module resultviewer)
addTable() (in module resultviewer)
AllGuiElements (in module ghi.const)
AnnotationsPath (in module ghi.const)
appendAnnotations() (in module navnode)
appendLog() (in module navnode)
appendNotes() (in module navnode)
appendSpreadsheet() (in module spreadsheet)
applyMarkerMap() (in module spreadsheet)
AppPath (in module ghi.const)
ArrayModeNative (in module ghi.const)
ArrayModeTyped (in module ghi.const)
asData() (in module resultviewer)
AssembliesPath (in module ghi.const)
asText() (in module resultviewer)
authority() (in module genomemap)

B

bayesCMethods() (in module spreadsheet)
BlockDetectGabriel (in module ghi.const)

C

CasesAndControls (in module ghi.const)
CasesOnly (in module ghi.const)
cell() (in module datamodel)
(in module spreadsheet)
childrenIDs() (in module navnode)
chooseDirectory() (in module ghi)
chooseFile() (in module ghi)
chooseMarkerMap() (in module ghi)
ChooseMultipleFiles (in module ghi.const)
ChooseSaveAs (in module ghi.const)
ChooseSingleFile (in module ghi.const)
clear() (in module genomemap)
clearCommonNames() (in module genomemap)
closeProject() (in module ghi)
cnamSegmentation() (in module spreadsheet)
col() (in module datamodel)
(in module spreadsheet)
colHeader() (in module tabular)
colHeaders() (in module datamodel)
(in module spreadsheet)
colIndex() (in module datamodel)
colIndexes() (in module datamodel)
(in module spreadsheet)
colState() (in module spreadsheet)
colSubset() (in module spreadsheet)
colType() (in module tabular)
CommonDataPath (in module ghi.const)
commonNames() (in module genomemap)
computeLD() (in module tabular)
computeLDStats() (in module tabular)
Confidence90 (in module ghi.const)
Confidence95 (in module ghi.const)
Confidence99 (in module ghi.const)
ContainsBinary (in module ghi.const)
ContainsGenetic (in module ghi.const)
ContainsInteger (in module ghi.const)
ContainsMappedGenetic (in module ghi.const)
ContainsMappedReal (in module ghi.const)
ControlsOnly (in module ghi.const)
convertAffyAnnotations() (in module ghi)
convertMarkerMap() (in module ghi)
coordSysId() (in module genomemap)
(in module trackreader)
coverageSpace() (in module trackreader)
createResultViewer() (in module ghi)
createScriptNode() (in module ghi)
createTabular() (in module genomebrowser)
createTopLevelSpreadsheet() (in module spreadsheet)
createTrack() (in module genomebrowser)

D

dataAutoDownload() (in module ghi)
dataFetchListing() (in module ghi)
dataFetchUrls() (in module ghi)
datamodel (module)
dataModel() (in module spreadsheet)
DataPath (in module ghi.const)
datasetbuilder (module)
dataSetBuilder() (in module ghi)
DataTypeBinary (in module ghi.const)
DataTypeCategorical (in module ghi.const)
DataTypeDouble (in module ghi.const)
DataTypeFloat (in module ghi.const)
DataTypeGenotypic (in module ghi.const)
DataTypeInteger (in module ghi.const)
date() (in module genomemap)
defaultCytobandUrl() (in module genomebrowser)
defaultGeneUrl() (in module genomebrowser)
DefaultGenomeMap (in module ghi.const)
defaultReferenceUrl() (in module genomebrowser)
deleteObject() (in module navnode)
deleteTrack() (in module genomebrowser)
dropMarkerMap() (in module spreadsheet)
DupFillLeft (in module ghi.const)
DupFillRight (in module ghi.const)
DupKeepBoth (in module ghi.const)

E

enableNewViewers() (in module ghi)
exit() (in module ghi)
exportCSV() (in module spreadsheet)
exportDSF() (in module spreadsheet)
exportGHD() (in module spreadsheet)
exportMarkerMap() (in module spreadsheet)
exportToFile() (in module spreadsheet)
exportTransposeToFile() (in module spreadsheet)

F

FieldIndexChr (in module ghi.const)
FieldIndexId (in module ghi.const)
fieldIndexMap() (in module trackreader)
FieldIndexStart (in module ghi.const)
FieldIndexStop (in module ghi.const)
fieldList() (in module trackreader)
fieldType() (in module trackreader)
FilterActive (in module ghi.const)
FilterActiveOnly (in module ghi.const)
FilterBinary (in module ghi.const)
FilterCategorical (in module ghi.const)
FilterDependent (in module ghi.const)
filterGenotypes() (in module spreadsheet)
FilterGenotypic (in module ghi.const)
FilterInt (in module ghi.const)
FilterMapped (in module ghi.const)
FilterQuantitative (in module ghi.const)
FilterReal (in module ghi.const)
findCol() (in module tabular)
findCols() (in module tabular)
findRow() (in module tabular)
findRows() (in module tabular)
finish() (in module datasetbuilder)
(in module markermapbuilderbyfield)
(in module markermapbuilderbymarker)
(in module progressdialog)
(in module trackwriter)
flush() (in module trackwriter)

G

genomeAssembly() (in module ghi)
genomebrowser (module)
genomemap (module)
genotypeAlleleCounts() (in module tabular)
genotypeAssociationTests() (in module spreadsheet)
genotypeColumnData() (in module tabular)
genotypePCA() (in module spreadsheet)
genotypeStatsByMarker() (in module spreadsheet)
genotypeStatsBySample() (in module spreadsheet)
getAnnotations() (in module navnode)
getColState() (in module spreadsheet)
getColType() (in module tabular)
getCurrentObject() (in module ghi)
getID() (in module navnode)
getMarkerMapChromosome() (in module tabular)
getMarkerMapField() (in module tabular)
getMarkerMapFieldCell() (in module tabular)
getMarkerMapFieldNames() (in module tabular)
getMarkerMapFieldTypes() (in module tabular)
getMarkerMapOffset() (in module tabular)
getMarkerMapOrientation() (in module tabular)
getMarkerMapPosition() (in module tabular)
getName() (in module navnode)
getObject() (in module ghi)
getOrderedChrList() (in module tabular)
getParent() (in module navnode)
getProperty() (in module ghi)
getRowState() (in module spreadsheet)
ghi (module)
GreaterOrEqual (in module ghi.const)
GreaterThan (in module ghi.const)

H

HapBlockAllMarkers (in module ghi.const)
HapBlockMovingWindow (in module ghi.const)
HapBlockPrecomputed (in module ghi.const)
HapImputeCHM (in module ghi.const)
HapImputeEM (in module ghi.const)
haplotypeAssociationTests() (in module spreadsheet)
haplotypeBlockDetection() (in module spreadsheet)
haplotypeCalculations() (in module spreadsheet)
haplotypeTrendRegression() (in module spreadsheet)
hasMarkerMap() (in module tabular)
hasNext() (in module trackreader)
hasPedFields() (in module datamodel)
(in module spreadsheet)
HeaderAutoDetect (in module ghi.const)
HeaderFirstRow (in module ghi.const)
HeaderGenerate (in module ghi.const)
hide() (in module navnode)
(in module progressdialog)

I

identityByDescentEstimation() (in module spreadsheet)
importBED() (in module ghi)
importCEL() (in module ghi)
importCHP() (in module ghi)
importCNCHP() (in module ghi)
importCNT() (in module ghi)
importData() (in module ghi)
importDSF() (in module ghi)
importFbatPedigree() (in module ghi)
importFbatPhenotype() (in module ghi)
importGHD() (in module ghi)
importIlluminaFinalReport() (in module ghi)
importMapAsSpreadsheet() (in module ghi)
importPED() (in module ghi)
importText() (in module ghi)
importTextPedigree() (in module ghi)
importTextPhenotype() (in module ghi)
importTPED() (in module ghi)
ImputeCHM (in module ghi.const)
ImputeEM (in module ghi.const)
indexOf() (in module trackreader)
intervalMode() (in module trackreader)
(in module trackwriter)
IntervalModeHalfOpen (in module ghi.const)
IntervalModeIndexed (in module ghi.const)
invertColState() (in module spreadsheet)
invertRowState() (in module spreadsheet)
isHidden() (in module progressdialog)
IsPedigree (in module ghi.const)
IsPrecomputedPca (in module ghi.const)
isValid() (in module datasetbuilder)

J

joinByRowLabels() (in module spreadsheet)

L

LessOrEqual (in module ghi.const)
LessThan (in module ghi.const)
localSourceList() (in module genomebrowser)

M

MapOrientationColumns (in module ghi.const)
MapOrientationNone (in module ghi.const)
MapOrientationRows (in module ghi.const)
markerMapBuilder() (in module ghi)
markermapbuilderbyfield (module)
markermapbuilderbymarker (module)
markerMapChromosomes() (in module tabular)
markerMapField() (in module tabular)
markerMapFieldCell() (in module tabular)
markerMapFieldNames() (in module tabular)
markerMapFieldTypes() (in module tabular)
markerMapFileName() (in module spreadsheet)
markerMapOffset() (in module tabular)
markerMapOrientation() (in module tabular)
MarkerMapPath (in module ghi.const)
markerMapPositions() (in module tabular)
MarkerMapsPath (in module ghi.const)
md5() (in module genomemap)
message() (in module ghi)
ModelAdditive (in module ghi.const)
ModelAllelic (in module ghi.const)
ModelDominant (in module ghi.const)
ModelGenotypic (in module ghi.const)
ModelRecessive (in module ghi.const)

N

navnode (module)
newProject() (in module ghi)
next() (in module trackreader)
nextFeatureSet() (in module trackreader)
nodeID() (in module navnode)
nodeName() (in module navnode)
nodeNotes() (in module navnode)
nodeTag() (in module navnode)
NoGuiElements (in module ghi.const)
numCols() (in module tabular)
numColsState() (in module spreadsheet)
numericAssociationTests() (in module spreadsheet)
numericPCA() (in module spreadsheet)
numericRegression() (in module spreadsheet)
numRows() (in module tabular)
numRowsState() (in module spreadsheet)

O

openFolder() (in module ghi)
openForRead() (in module genomebrowser)
openProject() (in module ghi)
openUrl() (in module ghi)
orderedChrList() (in module tabular)
OrientationHorizontal (in module ghi.const)
OrientationVertical (in module ghi.const)

P

parentNode() (in module navnode)
PcaCenteredByMarker (in module ghi.const)
PcaCenteredByMarkerAndSample (in module ghi.const)
PcaCenteredBySample (in module ghi.const)
PcaModelAdditive (in module ghi.const)
PcaModelDominant (in module ghi.const)
PcaModelRecessive (in module ghi.const)
PcaNormActual (in module ghi.const)
PcaNormDefault (in module ghi.const)
PcaNormNone (in module ghi.const)
PcaUncentered (in module ghi.const)
percentDone() (in module trackreader)
permuteRows() (in module spreadsheet)
plotColumns() (in module spreadsheet)
plotDependents() (in module spreadsheet)
plotHeatMap() (in module spreadsheet)
plotHistograms() (in module spreadsheet)
plotLD() (in module spreadsheet)
plotXY() (in module spreadsheet)
progressdialog (module)
progressDialog() (in module ghi)
ProgressOnly (in module ghi.const)
projectIsOpen() (in module ghi)
projectMaxNodeID() (in module ghi)
ProjectPath (in module ghi.const)
ProjectTempPath (in module ghi.const)
promptDialog() (in module ghi)
promptInteger() (in module ghi)
promptSpreadsheet() (in module ghi)
promptUser() (in module ghi)

Q

question() (in module ghi)

R

read() (in module trackreader)
readMode() (in module trackreader)
ReadModeExact (in module ghi.const)
ReadModeOverlap (in module ghi.const)
recodeGenotypes() (in module spreadsheet)
ReferenceAll (in module ghi.const)
ReferencePopulation (in module ghi.const)
ReferenceSubset (in module ghi.const)
RegressMovingWindow (in module ghi.const)
RegressPerColumn (in module ghi.const)
RegressSelected (in module ghi.const)
repr() (in module spreadsheet)
requiresPrecompute() (in module genomebrowser)
requireVersion() (in module ghi)
reset() (in module progressdialog)
resultviewer (module)
resumeLogging() (in module navnode)
rohGWAS() (in module spreadsheet)
rohNGS() (in module spreadsheet)
row() (in module datamodel)
(in module spreadsheet)
rowIndexes() (in module datamodel)
(in module spreadsheet)
rowLabel() (in module tabular)
rowLabels() (in module datamodel)
(in module spreadsheet)
rowState() (in module spreadsheet)
rowSubset() (in module spreadsheet)
runAutoPrecompute() (in module genomebrowser)
runPrecompute() (in module genomebrowser)

S

savePED() (in module spreadsheet)
saveProject() (in module ghi)
saveProjectAs() (in module ghi)
saveXml() (in module genomemap)
schema() (in module trackreader)
SegmentMaxPer10k (in module ghi.const)
SegmentMaxPerChr (in module ghi.const)
SegmentMultivariate (in module ghi.const)
SegmentOuputEveryColumn (in module ghi.const)
SegmentOuputFirstColumn (in module ghi.const)
SegmentUnivariate (in module ghi.const)
selectActiveRowsByCategories() (in module spreadsheet)
selectActiveRowsByColumnValue() (in module spreadsheet)
selectAllRowsByCategories() (in module spreadsheet)
selectAllRowsByColumnValue() (in module spreadsheet)
selectRowsByColumnBoolean() (in module spreadsheet)
selectRowsByColumnValue() (in module spreadsheet)
setColState() (in module spreadsheet)
setCoordSysId() (in module genomemap)
setDate() (in module genomemap)
setDoubleProgressMode() (in module progressdialog)
setIntervalMode() (in module trackreader)
(in module trackwriter)
setMarkerMap() (in module spreadsheet)
setMessage() (in module progressdialog)
setMinimumDuration() (in module progressdialog)
setMode() (in module progressdialog)
setName() (in module navnode)
setNodeTag() (in module navnode)
setProgress() (in module progressdialog)
setProgressMode() (in module progressdialog)
setReadMode() (in module trackreader)
setRowState() (in module spreadsheet)
setRowStateRandom() (in module spreadsheet)
setSecondaryMessage() (in module progressdialog)
setSecondaryProgress() (in module progressdialog)
setSecondaryTotalSteps() (in module progressdialog)
setStatusMode() (in module progressdialog)
setTaxId() (in module genomemap)
setTitle() (in module genomemap)
show() (in module navnode)
(in module progressdialog)
showCancel() (in module progressdialog)
sortByColAscending() (in module spreadsheet)
sortByColDescending() (in module spreadsheet)
sortByCustomOrder() (in module spreadsheet)
sortColIdx() (in module spreadsheet)
sortDirection() (in module spreadsheet)
species() (in module genomemap)
spreadsheet (module)
StatDPrime (in module ghi.const)
StateActive (in module ghi.const)
StateDependent (in module ghi.const)
StateInactive (in module ghi.const)
StatRSquared (in module ghi.const)
statusDialog() (in module ghi)
StepwiseBackward (in module ghi.const)
StepwiseForward (in module ghi.const)
stopLogging() (in module navnode)
(in module spreadsheet)
subsetColumns() (in module datamodel)
subsetRows() (in module datamodel)
subsetSpreadsheet() (in module datamodel)
SysDataPath (in module ghi.const)
SysGenomeMapPath (in module ghi.const)
SysTempPath (in module ghi.const)

T

tabular (module)
TagBlue (in module ghi.const)
TagGreen (in module ghi.const)
TagNone (in module ghi.const)
TagRed (in module ghi.const)
TagYellow (in module ghi.const)
taxId() (in module genomemap)
TestsPerBlock (in module ghi.const)
TestsPerHaplotype (in module ghi.const)
ThresholdFullP (in module ghi.const)
ThresholdLogFullModelP (in module ghi.const)
ThresholdLogMainP (in module ghi.const)
ThresholdMainP (in module ghi.const)
ThresholdRSquared (in module ghi.const)
title() (in module genomemap)
(in module trackreader)
tmpFileName() (in module ghi)
trackreader (module)
trackwriter (module)
transpose() (in module spreadsheet)
type() (in module genomemap)
(in module trackreader)
TypeBinary (in module ghi.const)
TypeCategorical (in module ghi.const)
TypeGenotypic (in module ghi.const)
TypeInteger (in module ghi.const)
TypeReal (in module ghi.const)

U

unsort() (in module spreadsheet)
UnsortedRows (in module ghi.const)
UserScriptsPath (in module ghi.const)
uuid() (in module trackreader)

V

value() (in module progressdialog)
Version (in module ghi.const)

W

wasCanceled() (in module progressdialog)
WindowDynamic (in module ghi.const)
WindowFixed (in module ghi.const)
write() (in module trackreader)
writeFeature() (in module trackwriter)

Z

zcol() (in module datamodel)
(in module spreadsheet)
zrow() (in module datamodel)
(in module spreadsheet)