Package index • Splatter

Package

Package description

splatter splatter-package: splatter: Simple Simulation of Single-cell RNA Sequencing Data

Parameters

Parameters functions and classes

newBASiCSParams() newKersplatParams() newLun2Params() newLunParams() newMFAParams() newPhenoParams() newSCDDParams() newSimpleParams() newSparseDCParams() newSplatParams() newSplatPopParams() newZINBParams(): New Params

getParam(): Get a parameter

getParams(): Get parameters

setParam(): Set a parameter

setParams(): Set parameters

BASiCSParams BASiCSParams-class: The BASiCSParams class

KersplatParams KersplatParams-class: The KersplatParams class

Lun2Params Lun2Params-class: The Lun2Params class

LunParams LunParams-class: The LunParams class

MFAParams MFAParams-class: The MFAParams class

Params Params-class: The Params virtual class

PhenoParams PhenoParams-class: The PhenoParams class

SCDDParams SCDDParams-class: The SCDDParams class

SimpleParams SimpleParams-class: The SimpleParams class

SplatParams SplatParams-class: The SplatParams class

SplatPopParams SplatPopParams-class: The SplatPopParams class

SparseDCParams SparseDCParams-class: The SparseDCParams class

ZINBParams ZINBParams-class: The ZINBParams class

Estimation

Functions for estimating parameters

BASiCSEstimate(): Estimate BASiCS simulation parameters

kersplatEstimate(): Estimate Kersplat simulation parameters

kersplatEstBCV(): Estimate Kersplat BCV parameters

kersplatEstLib(): Estimate Kersplat library size parameters

kersplatEstMean(): Estimate Kersplat means

lun2Estimate(): Estimate Lun2 simulation parameters

lunEstimate(): Estimate Lun simulation parameters

mfaEstimate(): Estimate mfa simulation parameters

phenoEstimate(): Estimate PhenoPath simulation parameters

scDDEstimate(): Estimate scDD simulation parameters

simpleEstimate(): Estimate simple simulation parameters

splatPopEstimate(): Estimate population/eQTL simulation parameters

splatPopEstimateEffectSize(): Estimate eQTL Effect Size parameters

splatPopEstimateMeanCV(): Estimate gene mean and gene mean variance parameters

splatEstBCV(): Estimate Splat Biological Coefficient of Variation parameters

splatEstDropout(): Estimate Splat dropout parameters

splatEstimate(): Estimate Splat simulation parameters

splatEstLib(): Estimate Splat library size parameters

splatEstMean(): Estimate Splat mean parameters

splatEstOutlier(): Estimate Splat expression outlier parameters

sparseDCEstimate(): Estimate SparseDC simulation parameters

zinbEstimate(): Estimate ZINB-WaVE simulation parameters

Simulation

Functions for simulating datasets

Splat simulation

Functions for the Splat simulation

splatSimulate() splatSimulateSingle() splatSimulateGroups() splatSimulatePaths(): Splat simulation

splatSimBatchCellMeans(): Simulate batch means

splatSimBatchEffects(): Simulate batch effects

splatSimBCVMeans(): Simulate BCV means

splatSimSingleCellMeans() splatSimGroupCellMeans() splatSimPathCellMeans(): Simulate cell means

splatSimGroupDE() splatSimPathDE(): Simulate group differential expression

splatSimDropout(): Simulate dropout

splatSimGeneMeans(): Simulate gene means

splatSimLibSizes(): Simulate library sizes

splatSimTrueCounts(): Simulate true counts

SplatPop simulation

Functions for the SplatPop simulation

splatPopSimulate(): splatPop simulation

splatPopAssignMeans(): Sample expression mean and variance for each gene

splatPopCleanSCE(): Clean up the population-scale SCE to remove redundant information

splatPopeQTLEffects(): Assign eGenes-eSNPs pairs and effect sizes.

splatPopGroupEffects(): Assign group-specific eQTL and DEGs.

splatPopParseGenes(): Generate population key matrix from random or gff provided gene information

splatPopParseVCF(): Format and subset genotype data from a VCF file.

splatPopQuantNorm(): Quantile normalize by sample to fit sc expression distribution.

splatPopQuantNormKey(): Add quantile normalized gene mean and cv info the eQTL key.

splatPopSimEffects(): Add eQTL effects to means matrix

splatPopSimGeneMeans(): Simulate gene means for splatPop

splatPopSimMeans(): Simulate mean gene expression matrix without eQTL effects

splatPopSimulateMeans(): splatPopSimulateMeans

splatPopSimulateSample(): splatPopSimulateSample simulation

splatPopSimulateSC(): splatPopSimulateSC

Other simulations

Functions for other simulation models

BASiCSSimulate(): BASiCS simulation

kersplatGenNetwork(): Generate Kersplat gene network

kersplatSample(): Kersplat sample

kersplatSelectRegs(): Select Kersplat regulators

kersplatSetup(): Kersplat setup

kersplatSimAmbientCounts(): Simulate Kersplat ambient counts

kersplatSimCellCounts(): Simulate Kersplat cell counts

kersplatSimCounts(): Simulate Kersplat final counts

kersplatSimCellMeans(): Simulate Kersplat cell means

kersplatSimGeneMeans(): Simulate Kersplat gene means

kersplatSimLibSizes(): Simulate Kersplat library sizes

kersplatSimPaths(): Simulate Kersplat paths

kersplatSimulate(): Kersplat simulation

lun2Simulate(): Lun2 simulation

lunSimulate(): Lun simulation

mfaSimulate(): MFA simulation

phenoSimulate(): PhenoPath simulation

scDDSimulate(): scDD simulation

simpleSimulate(): Simple simulation

sparseDCSimulate(): SparseDC simulation

zinbSimulate(): ZINB-WaVE simulation

Comparison functions

Functions for comparing datasets

compareSCEs(): Compare SingleCellExperiment objects

diffSCEs(): Diff SingleCellExperiment objects

makeCompPanel(): Make comparison panel

makeDiffPanel(): Make difference panel

makeOverallPanel(): Make overall panel

summariseDiff(): Summarise diffSCEs

Mock data

Simple mock datasets for tests and examples

mockBulkMatrix(): Generate mock bulk population scale expression data

mockBulkeQTL(): Generate mock eQTL mapping results

mockEmpiricalSet(): Generate set of "empirical" mock data

mockGFF(): Generate mock gff

mockVCF(): Generate mock vcf

Other exported functions

Additional functions exported by Splatter

addGeneLengths(): Add gene lengths

listSims(): List simulations

minimiseSCE(): Minimise SCE

splatPopParseEmpirical(): splatPopParseEmpirical