Parameters

Parameters functions and classes

newBASiCSParams newLun2Params newLunParams newMFAParams newPhenoParams newSCDDParams newSimpleParams newSparseDCParams newSplatParams newZINBParams

New Params

getParam

Get a parameter

getParams

Get parameters

setParam

Set a parameter

setParams

Set parameters

BASiCSParams

The BASiCSParams class

Lun2Params

The Lun2Params class

LunParams

The LunParams class

MFAParams

The MFAParams class

Params

The Params virtual class

PhenoParams

The PhenoParams class

SCDDParams

The SCDDParams class

SimpleParams

The SimpleParams class

SplatParams

The SplatParams class

SparseDCParams

The SparseDCParams class

ZINBParams

The ZINBParams class

Estimation

Functions for estimating parameters

BASiCSEstimate

Estimate BASiCS simulation parameters

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

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

BASiCSSimulate

BASiCS simulation

lun2Simulate

Lun2 simulation

lunSimulate

Lun simulation

mfaSimulate

MFA simulation

phenoSimulate

PhenoPath simulation

scDDSimulate

scDD simulation

simpleSimulate

Simple 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

splatSimulate splatSimulateSingle splatSimulateGroups splatSimulatePaths

Splat 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 diffSCESs

Other exported functions

Additional functions exported by Splatter

addFeatureStats

Add feature statistics

addGeneLengths

Add gene lengths

listSims

List simulations

Internals

Internal functions and helpers

bridge

Brownian bridge

expandParams

Expand parameters

getLNormFactors

Get log-normal factors

getPathOrder

Get path order

logistic

Logistic function

rbindMatched

Bind rows (matched)

setParamsUnchecked

Set parameters UNCHECKED

setParamUnchecked

Set a parameter UNCHECKED

showDFs

Show data.frame

showPP

Show pretty print

showValues

Show vales

winsorize

Winsorize vector