#' @title Function \code{simulation_duplicated}
#' @description simulation scenario made by simply duplicating the rows and columns of the Paschold data
#' @export
#' @return a list if pertinent scenario information
#' @param genes number of genes
#' @param libraries number of libraries
simulation_duplicated = function(genes = 3.5e4, libraries = 16){
data(paschold)
paschold = get("paschold")
gs = sample.int(nrow(paschold@counts), genes, replace = T)
ns = 0:(libraries -1) %% ncol(paschold@counts) + 1
group = (ns + (ns %% 2)) / 2
design = paschold@design[ns,]
counts = paschold@counts[gs, ns]
libnames = colnames(paschold@counts)
libnames = gsub("B73xMo17_Mo17xB73", "hybrids", libnames)
libnames = gsub("B73xMo17", "hybrid1", libnames)
libnames = gsub("Mo17xB73", "hybrid2", libnames)
libnames = gsub("B73", "parent1", libnames)
libnames = gsub("Mo17", "parent2", libnames)
libnames = gsub("_.*", "", libnames)
libnames = paste0(libnames[ns], "_", 1:libraries)
rownames(counts) = paste0("gene_", 1:genes)
colnames(counts) = rownames(design) = libnames
truth = list(
gs = gs,
ns = ns
)
supplement = list(
simulation = "duplicated",
group = group,
truth = truth
)
scenario = Scenario(
counts = counts,
design = design,
contrasts = paschold@contrasts,
bounds = paschold@bounds,
propositions = paschold@propositions,
supplement = supplement
)
list(scenario = scenario, analyses = list(), simulation = "duplicated")
}
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