Make simulated data for swish for examples/testing

Makes a small swish dataset for examples and testing. The first six genes have some differential expression evidence in the counts, with varying degree of inferential variance across inferential replicates (1-2: minor, 3-4: some, 5-6: substantial). The 7th and 8th genes have all zeros to demonstrate labelKeep.

makeSimSwishData(
  m = 1000,
  n = 10,
  numReps = 20,
  null = FALSE,
  meanVariance = FALSE,
  allelic = FALSE,
  diffAI = FALSE,
  dynamicAI = FALSE
)

Arguments

m: number of genes
n: number of samples
numReps: how many inferential replicates to generate
null: logical, whether to make an all null dataset
meanVariance: logical, whether to output only mean and variance of inferential replicates
allelic: logical, whether to make an allelic sim dataset
diffAI: logical, whether to make a differential allelic sim dataset
dynamicAI: logical, whether to make a dynamic allelic sim dataset

Value

a SummarizedExperiment

Examples


library(SummarizedExperiment)
y <- makeSimSwishData()
assayNames(y)
#>  [1] "counts"    "abundance" "length"    "infRep1"   "infRep2"   "infRep3"  
#>  [7] "infRep4"   "infRep5"   "infRep6"   "infRep7"   "infRep8"   "infRep9"  
#> [13] "infRep10"  "infRep11"  "infRep12"  "infRep13"  "infRep14"  "infRep15" 
#> [19] "infRep16"  "infRep17"  "infRep18"  "infRep19"  "infRep20"