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

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Documentation for package ‘LineagePulse’ version 1.13.0

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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