# Default null and alternative distributions, assuming different proportions
# of regulated genes
TOC(p0=c(0.90, 0.95, 0.99), legend.show=TRUE)
# The effect of sample size and effect size
par(mfrow=c(2,2))
TOC(p0=c(0.90, 0.95, 0.99), n=5, D=1)
TOC(p0=c(0.90, 0.95, 0.99), n=30, D=1)
TOC(p0=c(0.90, 0.95, 0.99), n=5, D=2)
TOC(p0=c(0.90, 0.95, 0.99), n=30, D=2)
# A wide null distribution that allows to disregard genes of small effect
# unspecified p means equal mixing proportions
ret = TOC(F0=list(D=c(-0.25,0,0.25)), main="Wide F0")
attr(ret,"param")$F0 # the null hypothesis
# An extended (and unsymmetric) alternative
ret = TOC(F1=list(D=c(-2,-1,1), p=c(1,2,2)), p0=0.95, main="Unsymmetric F1")
attr(ret,"param")$F1 # F1$p is normalized
# Unequal sample sizes
TOC(n1=10, n2=30)
# Curves for a paired t-test
TOC(paired=TRUE)
# The output contains all the x- and y-coordinates
ret = TOC(p0=c(0.90, 0.95, 0.99), main="Default settings")
dim(ret)
colnames(ret)
ret[1:10,]
# Additionally, the list of arguments that determine the experiment
attr(ret,"param")
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