makeSimSwishData: Make simulated data for swish for examples/testing

In mikelove/fishpond: Fishpond: downstream methods and tools for expression data

Make simulated data for swish for examples/testing

Description

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.

Usage

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)

mikelove/fishpond documentation built on Aug. 29, 2023, 2:45 p.m.