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

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accessors: LineagePulseObject accession methods

accessors: LineagePulseObject accession methods
In YosefLab/LineagePulse: Differential expression analysis and model fitting for single-cell RNA-seq data

Description Usage Arguments Value Author(s) Examples

Description

Get internal data of LineagePulse output object.

Usage

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dfAnnotationProc(objLP)

dfResults(objLP)

lsMuModelH0(objLP)

lsMuModelH1(objLP)

lsMuModelConst(objLP)

lsMuModelH0_NB(objLP)

lsMuModelH1_NB(objLP)

lsDispModelH0(objLP)

lsDispModelH1(objLP)

lsDispModelConst(objLP)

lsDispModelH0_NB(objLP)

lsDispModelH1_NB(objLP)

lsDropModel(objLP)

lsFitConvergence(objLP)

matCountsProc(objLP)

matWeights(objLP)

scaDFSplinesDisp(objLP)

scaDFSplinesMu(objLP)

strReport(objLP)

vecAllGenes(objLP)

vecConfoundersDisp(objLP)

vecConfoundersMu(objLP)

scaOmega(objLP)

boolFixedPopulations(objLP)

vecH0Pop(objLP)

vecNormConst(objLP)

strVersion(objLP)

strReport(objLP)

Arguments

objLP

(LineagePulse-Object) A LineagePulse output object to extract from.

Value

The internal data object specified by the function.

Author(s)

David Sebastian Fischer

Examples

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lsSimulatedData <- simulateContinuousDataSet(
    scaNCells = 10,
    scaNConst = 2,
    scaNLin = 2,
    scaNImp = 2,
    scaMumax = 100,
    scaSDMuAmplitude = 3,
    vecNormConstExternal=NULL,
    vecDispExternal=rep(20, 6),
    vecGeneWiseDropoutRates = rep(0.1, 6))
objLP <- runLineagePulse(
    counts = lsSimulatedData$counts,
    dfAnnotation = lsSimulatedData$annot,
    strMuModel = "impulse")
# get hidden objects within LineagePulse object
dfAnnotationProc <- dfAnnotationProc(objLP)
dfResults <- dfResults(objLP)
lsMuModelH0 <- lsMuModelH0(objLP)
lsMuModelH1 <- lsMuModelH1(objLP)
lsMuModelConst <- lsMuModelConst(objLP)
lsMuModelH0_NB <- lsMuModelH0_NB(objLP)
lsMuModelH1_NB <- lsMuModelH1_NB(objLP)
lsDispModelH0 <- lsDispModelH0(objLP)
lsDispModelH1 <- lsDispModelH1(objLP)
lsDispModelConst <- lsDispModelConst(objLP)
lsDropModel <- lsDropModel(objLP)
lsFitConvergence <- lsFitConvergence(objLP)
matCountDataProc <- matCountsProc(objLP)
matWeights <- matWeights(objLP)
scaDFSplinesDisp <- scaDFSplinesDisp(objLP) 
scaDFSplinesMu <- scaDFSplinesMu(objLP) 
strReport <- strReport(objLP) 
vecAllGenes <- vecAllGenes(objLP) 
vecConfoundersDisp <- vecConfoundersDisp(objLP) 
vecConfoundersMu <- vecConfoundersMu(objLP) 
scaOmega <- scaOmega(objLP) 
boolFixedPopulations <- boolFixedPopulations(objLP)
vecH0Pop <- vecH0Pop(objLP) 
vecNormConst <- vecNormConst(objLP) 
strVersion <- strVersion(objLP)

YosefLab/LineagePulse documentation built on May 6, 2019, 2:19 p.m.

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