Man pages for YosefLab/LineagePulse
Differential expression analysis and model fitting for single-cell RNA-seq data

accessorsLineagePulseObject accession methods
calcNormConstCompute size factors for a LineagePulse-object
calcPostDrop_MatrixCalculate posterior of drop-out
calcPostDrop_VectorCalculate posterior of drop-out
cash-LineagePulseObject-methodList-like accessor methods for LineagePulseObject: $
decompressDispByGeneCompute dispersion parameter estimates from mean parameter...
decompressDispByGeneMMCompute mean parameter estimate matrix from mean parameter...
decompressDropoutRateByCellCompute dropout rate parameter estimates from dropout rate...
decompressDropoutRateByGeneCompute dropout rate parameter estimates from dropout rate...
decompressMeansByGeneCompute mean parameter estimates from mean parameter model...
decompressMuByGeneMMCompute mean parameter estimate matrix from mean parameter...
evalDropoutModelCompute value of logistic dropout function given with scale...
evalDropoutModel_compCompiled function: evalDropoutModel
evalImpulseModelCompute value of impulse function given parameters.
evalImpulseModel_compCompiled function: evalImpulseModel
evalLogLikGeneWrapper for log likelihood of (zero-inflated) negative...
evalLogLikGeneMMWrapper for log likelihood of zero-inflated negative binomial...
evalLogLikMatrixWrapper for log likelihood of (zero-inflated) negative...
evalLogLikMuDispGeneFitCost function (zero-inflated) negative binomial model for...
evalLogLikMuDispGeneFit_compCompiled function: evalLogLikMuDispGeneFit
evalLogLikNBCompute loglikelihood of negative binomial model for a vector...
evalLogLikNB_compCompiled function: evalLogLikNB
evalLogLikPiZINB_ManyCellsCost function zero-inflated negative binomial model for...
evalLogLikPiZINB_ManyCells_compCost function zero-inflated negative binomial model for...
evalLogLikPiZINB_SingleCellCost function zero-inflated negative binomial model for...
evalLogLikPiZINB_SingleCell_compCost function zero-inflated negative binomial model for...
evalLogLikZINBCompute loglikelihood of zero-inflated negative binomial...
evalLogLikZINB_compCompiled function: evalLogLikZINB
fitLPModelsFit all models necessary for LineagePulse
fitModelFit (zero-inflated) negative binomial model to data
fitMuDispCoordinate mean and dispersion parameter co-estimation step
fitMuDispGeneOptim wrapper for gene-wise models other than mixture model.
fitMuDispGeneImpulseMultiple initilalisation wrapper for impulse mean model
fitMuDispGeneMMOptim wrapper for gene-wise models other than mixture model.
fitPiGlobal wrapper for fitting of all drop-out models
fitPi_ManyCellsOptim wrapper for drop-out model fitting on many cells
fitPi_SingleCellOptim wrapper for drop-out model fitting on single cell
getFitsDispersionGet dispersion model fits
getFitsDropoutGet drop-out model fits
getFitsMeanGet mean model fits
getNormDataReturn depth and batch corrected data
getPostDropGet posteriors of drop-out
initDispModelInitialise dispersion model container object
initDropModelInitialise drop-out model container object
initialiseImpulseParametersEstimate impulse model parameter initialisations
initMuModelInitialise mean model container object
LineagePulseObject-classContainer class for LineagePulse output
LPsettersLineagePulseObject setters
names-LineagePulseObject-methodList-like accessor methods for LineagePulseObject: names()
plotCellDensityPlot density of cells in continuous covariate
plotGenePlot counts and model for one gene
processSCDataPrepare single cell data for analysis
runDEAnalysisDifferential expression analysis
runLineagePulseLineagePulse wrapper: Differential expression analysis on...
simulateContinuousDataSetSimulate a data set for LinagePulse Simulates a data set with...
sortGeneTrajectoriesCluster expression mean trajectories
sub-sub-LineagePulseObject-character-missing-methodList-like accessor methods for LineagePulseObject: names()
testDropoutTest for existance of drop-out with log-likelihood ratio test
writeReportPrint LineagePulse report
YosefLab/LineagePulse documentation built on March 21, 2018, 8:54 p.m.