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Installation

library(devtools)
install_github("ArtemisZhao/INTRIGUE/R_src")

Example dataset

library(INTRIGUE)
data("heterodata")

This is a simulated datasets with n=5000 experimental units (e.g., genes) and m=2 replicates. The true proportions for the null, the reproducible and the irreproducible signal categories are 0.80, 0.18, 0.02, respectively.

CEFN prior

##for convenience, only test on first 100 units 
hetero.out.cefn<-hetero(heterodata[1:100,],fdr.level=0.05)

META prior

hetero.out.meta<-hetero(heterodata[1:100,],use_cefn=FALSE,fdr.level=0.05)

Outcome

names(hetero.out.cefn)

## overall proportion
print(hetero.out$est_prop)

Return a list containing the following,

1. gridweight: estimated weight on each grid point.

2. ind_prob: individual probability of falling into three groups.

3. est_prop: estimated overall proportion for three groups.

4. lfdr: false discovery rate.

5. significant: decision based on the fdr.level in the input.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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