getFitsDispersion: Get dispersion model fits

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

Description

Return dispersion model fits per gene and cell as matrix for chosen model.

Usage

getFitsDispersion(lsDispModel, vecGeneIDs = NULL)

Arguments

lsDispModel	(list) Object containing description of gene-wise dispersion parameter models.
vecGeneIDs	(vector of strings) Gene IDs for which dispersion model fits are to be extracted.

Value

(numeric matrix genes x cells) Dispersion parameter fits.

Author(s)

David Sebastian Fischer

Examples

lsSimulatedData <- simulateContinuousDataSet(
    scaNCells = 20,
    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 dispersion parameter fits on alternative model:
# Use H1 model fits.
vecDispersionFits <- getFitsDispersion(
     lsDispModel = lsDispModelH1(objLP),
     vecGeneIDs = rownames(lsSimulatedData$counts)[1])

LineagePulse documentation built on Nov. 8, 2020, 7:01 p.m.