API for rohan-shah/mpMap2
Multi-parent RIL genetic analysis

Global functions
+,geneticData,assignFounderPattern-method Man page
+,geneticData,assignFounderPatternPrototype-method Man page
+,geneticData,biparentalDominant-method Man page
+,geneticData,fixedNumberOfFounderAlleles-method Man page
+,geneticData,multiparentSNP-method Man page
+,geneticData,multiparentSNPPrototype-method Man page
+,geneticData,normalPhenotype-method Man page
+,mpcross,assignFounderPattern-method Man page
+,mpcross,assignFounderPatternPrototype-method Man page
+,mpcross,biparentalDominant-method Man page
+,mpcross,fixedNumberOfFounderAlleles-method Man page
+,mpcross,mpcross-method Man page
+,mpcross,multiparentSNP-method Man page
+,mpcross,multiparentSNPPrototype-method Man page
+,mpcross,normalPhenotype-method Man page
+,mpcross,removeHets-method Man page
+,mpcrossMapped,assignFounderPattern-method Man page
+,mpcrossMapped,assignFounderPatternPrototype-method Man page
+,mpcrossMapped,mpcrossMapped-method Man page
+,mpcrossRF,mpcross-method Man page
+,mpcrossRF,mpcrossRF-method Man page
[,rawSymmetricMatrix,index,index,logical-method Man page
[,rawSymmetricMatrix,index,index,missing-method Man page
[,rawSymmetricMatrix,matrix,missing,missing-method Man page
[,rawSymmetricMatrix,missing,missing,missing-method Man page
addExtraMarkerFromRawCall Man page Source code
addExtraMarkers Man page Source code
as.mpInterval Source code
as.mpInterval.mpInterval Source code
as.mpInterval.mpMarker Source code
assignFounderPattern Source code
assignFounderPatternPrototype Source code
assignFounderPatternPrototypeInternal Source code
backcrossPedigree Source code
biparentalDominant Man page Source code
canSkipValidityInitialize Source code
changeMarkerPosition Source code
checkCompatibleGeneticData Source code
checkDetailedPedigree Source code
checkGeneticData Source code
checkGeneticDataList Source code
checkHets Source code
checkImputedData Source code
checkLG Source code
checkMap Source code
checkMpcross Source code
checkMpcrossLG Source code
checkMpcrossMapped Source code
checkMpcrossRF Source code
checkPedigree Source code
checkPedigreeGraph Source code
checkProbabilities Source code
checkRF Source code
checkRawSymmetricMatrix Source code
clusterOrderCross Source code
combineGenotypes Source code
combineKeepRF Source code
compressedProbabilities Source code
computeAllEpistaticChiSquared Source code
computeGenotypeProbabilities Source code
computeGenotypeProbabilitiesInternal Source code
condition Source code
createSNPTemplate Source code
designMat Source code
detailedPedigree Man page Source code
detailedPedigree-class Man page
eightParentPedigreeImproperFunnels Man page Source code
eightParentPedigreeImproperFunnelsPrototype Source code
eightParentPedigreeRandomFunnels Man page Source code
eightParentPedigreeRandomFunnelsPrototype Source code
eightParentPedigreeSingleFunnel Man page Source code
eightParentPedigreeSingleFunnelPrototype Source code
estimateMap Man page Source code
estimateMapFromImputation Source code
estimateMapInternal Source code
estimateRF Man page Source code
estimateRFInternal Source code
estimateRFSingleDesign Source code
estimateRFSingleDesignInternal Source code
expand Source code
expandedProbabilitiesFinite Source code
expandedProbabilitiesInfinite Source code
exportMapToPretzl Source code
extraImputationPoints Source code
f2Pedigree Man page Source code
fixedNumberOfFounderAlleles Source code
formGroups Man page Source code
fourParentPedigreeRandomFunnels Man page Source code
fourParentPedigreeRandomFunnelsPrototype Source code
fourParentPedigreeSingleFunnel Man page Source code
fourParentPedigreeSingleFunnelPrototype Source code
fromMpMap Source code
fullHetData Source code
generateGridPositions Source code
generateIntervalMidPoints Source code
getAllFunnels Source code
getAllFunnelsIncAIC Source code
getChromosomes Source code
getIntercrossingAndSelfingGenerations Source code
getPositions Source code
haldane Man page
haldaneToRf Man page Source code
hetsForSNPMarkers Source code
impute Source code
imputeFounders Man page Source code
infiniteSelfing Source code
inheritsNewMpcrossArgument Source code
isDetailedPedigreeArgument Source code
isHetDataArgument Source code
isIntegerMatrixArgument Source code
isMapArgument Source code
isMpMapPedigreeArgument Source code
isNewMpcrossLGArgument Source code
isNewMpcrossMappedArgument Source code
isNewMpcrossRFArgument Source code
isNumericMatrixArgument Source code
isNumericVectorListArgument Source code
isOldMpMapMpcrossArgument Source code
isPedigreeArgument Source code
jitterMap Source code
kosambi Man page
kosambiToRf Man page Source code
linesByNames Source code
listCodingErrors Source code
listCodingErrorsMpMap Source code
mapFunctions Man page
mpcross Source code
mpcrossMapped Source code
multiparentSNP Source code
multiparentSNPKeepHets Source code
multiparentSNPPrototype Source code
multiparentSNPPrototypeKeepHets Source code
multiparentSNPPrototypeRemoveHets Source code
multiparentSNPRemoveHets Source code
nonNegativeIntegerArgument Source code
normalPhenotype Source code
orderCross Source code
pedigree Source code Source code
pedigree-class Man page
pedigreeToGraph Source code
plotMosaic Source code
plotProbabilities Source code
positiveIntegerArgument Source code
print.mpcross Source code
print.mpcrossLG Source code
print.mpcrossRF Source code
purdyToPedigree Source code
rcpp_collect_warnings Source code
rcpp_error_recorder Source code
rcpp_warning_recorder Source code
removeHets Source code
reorderPedigree Source code
reverseChromosomes Source code
rfToHaldane Man page Source code
rfToKosambi Man page Source code
rilPedigree Man page Source code
simulateMPCross Man page Source code
singleLocusProbabilities Source code
sixteenParentPedigreeRandomFunnels Man page Source code
sixteenParentPedigreeRandomFunnelsPrototype Source code
splitVector Source code Source code
stripPedigree Source code
testDistortion Source code
toMpMap Source code
transposeProbabilities Source code
twoParentPedigree Man page Source code
rohan-shah/mpMap2 documentation built on Jan. 22, 2018, 12:15 a.m.