evaluateSim: Compute the performance related metrics from simulation...

In bvieth/powsimR: Power Simulations for RNA-sequencing

Compute the performance related metrics from simulation results.

Description

This function takes the simulation output from simulateDE and computes several metrics that give an indication of the simulation setup performance.

Usage

evaluateSim(simRes)

Arguments

simRes

The result from simulateDE.

Value

A list with the following entries:

LogFoldChange	The absolute mean error (MAE), root mean square error (RMSE) and root mean square residual error of a robust linear model (rRMSE, rlm) of log fold change differences between estimated and simulated. Furthermore, the fraction of missing entries (NAFraction) for MAE annd RMSE.
SizeFactors	The median absolute deviation (MAD) between the simulated and estimated size factors, the root mean square residual error of a robust linear model (rRMSE, rlm) and the group-specific ratio between simulated and estimated size factors (GroupX).

Author(s)

Beate Vieth

See Also

estimateParam for negative binomial parameters, Setup for setting up simulation parameters and simulateDE for simulating differential expression

Examples

## Not run: 
# estimate gene parameters
data("SmartSeq2_Gene_Read_Counts")
Batches = data.frame(Batch = sapply(strsplit(colnames(SmartSeq2_Gene_Read_Counts), "_"), "[[", 1),
                     stringsAsFactors = F,
                     row.names = colnames(SmartSeq2_Gene_Read_Counts))
data("GeneLengths_mm10")
estparam_gene <- estimateParam(countData = SmartSeq2_Gene_Read_Counts,
                               readData = NULL,
                               batchData = Batches,
                               spikeData = NULL, spikeInfo = NULL,
                               Lengths = GeneLengths_mm10, MeanFragLengths = NULL,
                               RNAseq = 'singlecell', Protocol = 'Read',
                               Distribution = 'ZINB', Normalisation = "scran",
                               GeneFilter = 0.1, SampleFilter = 3,
                               sigma = 1.96, NCores = NULL, verbose = TRUE)
# define log fold change
p.lfc <- function(x) sample(c(-1,1), size=x,replace=T)*rgamma(x, shape = 1, rate = 2)
# set up simulations
setupres <- Setup(ngenes = 10000, nsims = 10,
                  p.DE = 0.1, pLFC = p.lfc,
                  n1 = c(20,50,100), n2 = c(30,60,120),
                  Thinning = c(1,0.9,0.8), LibSize = 'given',
                  estParamRes = estparam_gene,
                  estSpikeRes = NULL,
                  DropGenes = FALSE,
                  sim.seed = 66437, verbose = TRUE)
# run simulation
simres <- simulateDE(SetupRes = setupres,
                     Prefilter = "FreqFilter",
                     Imputation = NULL,
                     Normalisation = 'scran', Label = 'none',
                     DEmethod = "limma-trend", DEFilter = FALSE,
                     NCores = NULL, verbose = TRUE)

# evaluation
evalsimres <- evaluateSim(simRes = simres)
plotEvalSim(evalRes = evalsimres, Annot = TRUE)
plotTime(evalRes = evalsimres, Annot = TRUE)

## End(Not run)

bvieth/powsimR documentation built on Aug. 19, 2023, 7:48 p.m.