Purpose this is a demonstration of functionality *overview of features and availability
library(msiCompare)
library(Cardinal)
conditions <- ifelse((expand.grid(x=1:30, y=1:30)$x %in% (1+floor(30/5)):(30-floor(30/5)) & expand.grid(x=1:30, y=1:30)$y %in% (1+floor(30/5)):(30-floor(30/5))), 2, 1) s <- simSingle( reps = 3, diff = log2(1.5), tau2 = 0.1, sig2 = 0.1, seed = 8372, size1 = 30, center.pattern = T, pattern = conditions )
summary(s)
image(s$simSet, feature = 1)
s_multi <- simMulti( sampleVar = 0.1, reps = 1, diff = log2(1.5), tau2 = 0.1, sig2 = 0.1, seed = 8372, size1 = 30, size2 = 30^2, numHealthy = 3, numDisease = 3) image(s_multi$simSet, feature = 1, layout = c(3,2))
fitHBSM <- compareMSI(msset = s_multi$simSet, conditionOfInterest = s_multi$simSet$diagnosis, techRep = s_multi$simSet$sample, feature = 1, nsim = 5000, burnin=2500, trace = F, dropZeros = T) fitHBSM$Feature1$gamma
note hiearchical centering bfdr adjustment
summary(lm(c(spectra(s_multi$simSet)[1,]) ~ s_multi$simSet$diagnosis))
p_averaging(s_multi$simSet)
fit_spautolm <- cass(msset = s$simSet, roiFactor = factor(s$simSet$diagnosis), logscale = F, thresholds = 1:5) fit_spautolm$results$CAR_AIC_min_pvalues
cite show their model
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