Parameters

Parameters functions and classes

getParam

Get a parameter

getParams

Get parameters

The Lun2Params class

The LunParams class

newLun2Params newLunParams newSCDDParams newSimpleParams newSplatParams

New Params

The Params virtual class

The SCDDParams class

The SimpleParams class

The SplatParams class

setParam

Set a parameter

setParams

Set parameters

Estimation

Functions for estimating parameters

lun2Estimate

Estimate Lun2 simulation parameters

lunEstimate

Estimate Lun 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

Simulation

Functions for simulating datasets

lun2Simulate

Lun2 simulation

lunSimulate

Lun 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

Comparison functions

Functions for comparing datasets

compareSCESets

Compare SCESet objects

diffSCESets

Diff SCESet objects

makeCompPanel

Make comparison panel

makeDiffPanel

Make difference panel

makeOverallPanel

Make overall panel

summariseDiff

Summarise diffSCESets

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

showPP

Show pretty print

winsorize

Winsorize vector