Differential expression analysis and model fitting for single-cell RNA-seq data

Documentation for package ‘LineagePulse’ version 1.21.0

Help Pages

A B C D E F G I L M N P R S T V W misc

-- A --

accessors

LineagePulseObject accession methods

-- B --

boolFixedPopulation	LineagePulseObject accession methods
boolFixedPopulation<-	LineagePulseObject setters
boolFixedPopulations	LineagePulseObject accession methods

-- C --

calcNormConst	Compute size factors for a LineagePulse-object
calcPostDrop_Matrix	Calculate posterior of drop-out
calcPostDrop_Vector	Calculate posterior of drop-out

-- D --

decompressDispByGene	Compute dispersion parameter estimates from mean parameter model for a gene
decompressDispByGeneMM	Compute mean parameter estimate matrix from mean parameter model for a gene (strDispModel == "MM")
decompressDropoutRateByCell	Compute dropout rate parameter estimates from dropout rate model for a cell
decompressDropoutRateByGene	Compute dropout rate parameter estimates from dropout rate model for a gene
decompressMeansByGene	Compute mean parameter estimates from mean parameter model for a gene
decompressMuByGeneMM	Compute mean parameter estimate matrix from mean parameter model for a gene (strMuModel == "MM")
dfAnnotationProc	LineagePulseObject accession methods
dfAnnotationProc<-	LineagePulseObject setters
dfResults	LineagePulseObject accession methods
dfResults<-	LineagePulseObject setters

-- E --

evalDropoutModel	Compute value of logistic dropout function given with scale boundaries
evalDropoutModel_comp	Compiled function: evalDropoutModel
evalImpulseModel	Compute value of impulse function given parameters.
evalImpulseModel_comp	Compiled function: evalImpulseModel
evalLogLikGene	Wrapper for log likelihood of (zero-inflated) negative binomial model for a vector of counts.
evalLogLikGeneMM	Wrapper for log likelihood of zero-inflated negative binomial model for a vector of counts.
evalLogLikMatrix	Wrapper for log likelihood of (zero-inflated) negative binomial model for a matrix of counts (parallelised).
evalLogLikMuDispGeneFit	Cost function (zero-inflated) negative binomial model for mean and dispersion model fitting
evalLogLikMuDispGeneFit_comp	Compiled function: evalLogLikMuDispGeneFit
evalLogLikNB	Compute loglikelihood of negative binomial model for a vector of counts.
evalLogLikNB_comp	Compiled function: evalLogLikNB
evalLogLikPiZINB_ManyCells	Cost function zero-inflated negative binomial model for drop-out fitting for many cells
evalLogLikPiZINB_ManyCells_comp	Cost function zero-inflated negative binomial model for drop-out fitting
evalLogLikPiZINB_SingleCell	Cost function zero-inflated negative binomial model for drop-out fitting
evalLogLikPiZINB_SingleCell_comp	Cost function zero-inflated negative binomial model for drop-out fitting
evalLogLikZINB	Compute loglikelihood of zero-inflated negative binomial model for a vector of counts.
evalLogLikZINB_comp	Compiled function: evalLogLikZINB

-- F --

fitLPModels	Fit all models necessary for LineagePulse
fitModel	Fit (zero-inflated) negative binomial model to data
fitMuDisp	Coordinate mean and dispersion parameter co-estimation step
fitMuDispGene	Optim wrapper for gene-wise models other than mixture model.
fitMuDispGeneImpulse	Multiple initilalisation wrapper for impulse mean model
fitMuDispGeneMM	Optim wrapper for gene-wise models other than mixture model.
fitPi	Global wrapper for fitting of all drop-out models
fitPi_ManyCells	Optim wrapper for drop-out model fitting on many cells
fitPi_SingleCell	Optim wrapper for drop-out model fitting on single cell
function	LineagePulse wrapper: Differential expression analysis on scRNA-seq

-- G --

getFitsDispersion	Get dispersion model fits
getFitsDropout	Get drop-out model fits
getFitsMean	Get mean model fits
getNormData	Return depth and batch corrected data
getPostDrop	Get posteriors of drop-out

-- I --

initDispModel	Initialise dispersion model container object
initDropModel	Initialise drop-out model container object
initialiseImpulseParameters	Estimate impulse model parameter initialisations
initMuModel	Initialise mean model container object

-- L --

LineagePulse	LineagePulse wrapper: Differential expression analysis on scRNA-seq
LineagePulseObject-class	Container class for LineagePulse output
LPsetters	LineagePulseObject setters
lsDispModelConst	LineagePulseObject accession methods
lsDispModelConst<-	LineagePulseObject setters
lsDispModelH0	LineagePulseObject accession methods
lsDispModelH0<-	LineagePulseObject setters
lsDispModelH0_NB	LineagePulseObject accession methods
lsDispModelH0_NB<-	LineagePulseObject setters
lsDispModelH1	LineagePulseObject accession methods
lsDispModelH1<-	LineagePulseObject setters
lsDispModelH1_NB	LineagePulseObject accession methods
lsDispModelH1_NB<-	LineagePulseObject setters
lsDropModel	LineagePulseObject accession methods
lsDropModel<-	LineagePulseObject setters
lsFitConvergence	LineagePulseObject accession methods
lsFitConvergence<-	LineagePulseObject setters
lsMuModelConst	LineagePulseObject accession methods
lsMuModelConst<-	LineagePulseObject setters
lsMuModelH0	LineagePulseObject accession methods
lsMuModelH0<-	LineagePulseObject setters
lsMuModelH0_NB	LineagePulseObject accession methods
lsMuModelH0_NB<-	LineagePulseObject setters
lsMuModelH1	LineagePulseObject accession methods
lsMuModelH1<-	LineagePulseObject setters
lsMuModelH1_NB	LineagePulseObject accession methods
lsMuModelH1_NB<-	LineagePulseObject setters

-- M --

main	LineagePulse wrapper: Differential expression analysis on scRNA-seq
matCountsProc	LineagePulseObject accession methods
matCountsProc<-	LineagePulseObject setters
matWeights	LineagePulseObject accession methods
matWeights<-	LineagePulseObject setters

-- N --

names-method

List-like accessor methods for LineagePulseObject: names()

-- P --

plotCellDensity	Plot density of cells in continuous covariate
plotGene	Plot counts and model for one gene
processSCData	Prepare single cell data for analysis

-- R --

runDEAnalysis	Differential expression analysis
runLineagePulse	LineagePulse wrapper: Differential expression analysis on scRNA-seq

-- S --

scaDFSplinesDisp	LineagePulseObject accession methods
scaDFSplinesDisp<-	LineagePulseObject setters
scaDFSplinesMu	LineagePulseObject accession methods
scaDFSplinesMu<-	LineagePulseObject setters
scaOmega	LineagePulseObject accession methods
scaOmega<-	LineagePulseObject setters
simulateContinuousDataSet	Simulate a data set for LinagePulse Simulates a data set with genes with constant and impulse expression traces. Expression strength and variation in impulse like traces are parameterised and random. All temporary files are saved into dirOutSimulation and only the objects necessary for running LineagePulse (the count matrix and the continuous covariate vector are returned). The remaining objects representing hidden parameters can be used to evaluate parameter estimates. Cells are distributed uniformly in the continuous covariate.
sortGeneTrajectories	Cluster expression mean trajectories
strReport	LineagePulseObject accession methods
strReport<-	LineagePulseObject setters
strVersion	LineagePulseObject accession methods
strVersion<-	LineagePulseObject setters

-- T --

testDropout

Test for existance of drop-out with log-likelihood ratio test

-- V --

vecAllGenes	LineagePulseObject accession methods
vecAllGenes<-	LineagePulseObject setters
vecConfoundersDisp	LineagePulseObject accession methods
vecConfoundersDisp<-	LineagePulseObject setters
vecConfoundersMu	LineagePulseObject accession methods
vecConfoundersMu<-	LineagePulseObject setters
vecH0Pop	LineagePulseObject accession methods
vecH0Pop<-	LineagePulseObject setters
vecNormConst	LineagePulseObject accession methods
vecNormConst<-	LineagePulseObject setters

-- W --

wrapper,	LineagePulse wrapper: Differential expression analysis on scRNA-seq
writeReport	Print LineagePulse report

-- misc --

$-method	List-like accessor methods for LineagePulseObject: $
[[-method	List-like accessor methods for LineagePulseObject: names()
`boolFixedPopulation<-`	LineagePulseObject setters
`dfAnnotationProc<-`	LineagePulseObject setters
`dfResults<-`	LineagePulseObject setters
`lsDispModelConst<-`	LineagePulseObject setters
`lsDispModelH0<-`	LineagePulseObject setters
`lsDispModelH0_NB<-`	LineagePulseObject setters
`lsDispModelH1<-`	LineagePulseObject setters
`lsDispModelH1_NB<-`	LineagePulseObject setters
`lsDropModel<-`	LineagePulseObject setters
`lsFitConvergence<-`	LineagePulseObject setters
`lsMuModelConst<-`	LineagePulseObject setters
`lsMuModelH0<-`	LineagePulseObject setters
`lsMuModelH0_NB<-`	LineagePulseObject setters
`lsMuModelH1<-`	LineagePulseObject setters
`lsMuModelH1_NB<-`	LineagePulseObject setters
`matCountsProc<-`	LineagePulseObject setters
`matWeights<-`	LineagePulseObject setters
`scaDFSplinesDisp<-`	LineagePulseObject setters
`scaDFSplinesMu<-`	LineagePulseObject setters
`scaOmega<-`	LineagePulseObject setters
`strReport<-`	LineagePulseObject setters
`strVersion<-`	LineagePulseObject setters
`vecAllGenes<-`	LineagePulseObject setters
`vecConfoundersDisp<-`	LineagePulseObject setters
`vecConfoundersMu<-`	LineagePulseObject setters
`vecH0Pop<-`	LineagePulseObject setters
`vecNormConst<-`	LineagePulseObject setters