hetero: Heterogeneity Evaluation
In INTRIGUE: Quantify and Control Reproducibility in High-Throughput Experiments

Description Usage Arguments Value Examples

View source: R/hetero.R

Evaluating the overall and individually heterogeneity and reproducibility for the given individuals(units) shared in different replicates.

hetero(
  data,
  use_cefn = TRUE,
  rep = NULL,
  irre = NULL,
  phi_min = NULL,
  phi_max = NULL,
  sq_em_tol = 1e-04,
  fdr.level = NULL,
  sample_size = NULL
)

`data`	A dataset which is constructed by pairs of coefficient values β and standard errors se(β).
`use_cefn`	A boolean, denoting whether to use CEFN prior. If the value is TRUE, CEFN prior is used, else, META prior is applied. The default value is TRUE.
`rep`	A vector, denoting all the k^2 (under CEFN prior) or r (under META prior) values constructing the reproducible signals. If not specified, the default one is c(0.105,0.260,0.369), which corresponds to the several prior values satisfy that Pr(β_{i,1}, β_{i,2} have a same sign)=0.99, 0.975, 0.95 for CEFN prior.
`irre`	A vector, denoting all the k^2 or r values constructing the irreproducible signals. If not specified, the default one is c(2.198, 3.636, 6.735), which corresponds to the several prior values satisfy that Pr(β_{i,1}, β_{i,2} have a same sign)=0.75, 0.70, 0.65 for CEFN prior.
`phi_min`	A value which determines the maximum phi. If not specified, will be constructed from the input datasets.
`phi_max`	A value which determines the minimum phi. If not specified, will be constructed from the input datasets.
`sq_em_tol`	A small, positive scalar that determines when iterations should be terminated in squarem algorithm. The default value is 1e-4.
`fdr.level`	The user-defined rejection level for false discovery rate.
`sample_size`	The user-defined sample size.

A list with the following components:

`gridweight`	The final optimal weight vector evaluated on each grid point.
`ind_prob`	A matrix denoting the converged probability for each individual being inside the three different groups, namely, the null, the reproducible and the irreproducible group.
`est_prop`	The estimated proportion value for the three different groups, namely, the null, the reproducible and the irreproducible group.
`lfdr`	The local false discovery rate based on the null hyppthesis of unit belonging to H_R, reproducible group. lfdr=1-Pr(H_R)
`significant`	If fdr.level is specified, a significant object recording True or False will be returned

data("heterodata")

hetero.out<-hetero(heterodata,fdr.level=0.05)
names(hetero.out)
print(hetero.out$est_prop)


## for CRAN check
hetero.out<-hetero(heterodata[1:100,],fdr.level=0.05)