#' @title sim single tissue
#' @description sim single tissue
#' @param tau2 asfasdf
#' @return sim
#' @import Cardinal
#' @import mvtnorm
#' @import spam
#' @export
#'
simSingle <- function(
reps = 1,
diff = log2(1.5),
tau2 = 1,
sig2 = .1,
seed = 100,
size1 = 15,
center.pattern = F,
pattern = ifelse((expand.grid(x=1:size1, y=1:size1)$x %in% (1+floor(size1/5)):(size1-floor(size1/5)) & expand.grid(x=1:size1, y=1:size1)$y %in% (1+floor(size1/5)):(size1-floor(size1/5))), 2, 1)
){
size2 <- size1^2
diagnosis <- ifelse(pattern == 2, "Healthy", "Disease")
coord <- expand.grid(x=1:size1, y=1:size1)
samples <-sampleCAR(condDiff = diff,
coord = expand.grid(x=1:size1, y=1:size1),
sig2 = sig2, tau2 = tau2,
rho = .9999, nrep=reps,
pattern = pattern,
save = F, randomSeed = seed, center.pattern = center.pattern)
simSet <- MSImageSet(spectra = matrix(samples,ncol = size2),
coord = expand.grid(x=1:size1, y=1:size1))
pData(simSet)$diagnosis <- diagnosis
pData(simSet)$sample <- factor(rep("1", size2))
#image(simSet, feature=1)
return(list(simSet = simSet,
reps = reps,
diff = diff,
tau2 = tau2,
sig2 = sig2,
seed = seed,
size1 = size1,
size2 = size2
))
}
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