gIDR: Estimate IDR with a General Mixture Model

In eCV: Enhanced Coefficient of Variation and IDR Extensions for Reproducibility Assessment

Estimate IDR with a General Mixture Model

Description

This function builds upon 'idr::est.IDR' to extend the Li et al. (2011) copula mixture model to accommodate an arbitrary number of replicates. The term "General" in this context alludes to the assumption of a general multivariate Normal distribution of dimension "n," equal to the number of sample replicates. This assumption essentially allows the pseudo-likelihood approach in Li et al. (2011) to be extended to any number of replicates. This is achieved by modifying the "E" and "M" steps of an expectation maximization algorithm to use a multivariate Normal Distribution instead.

Usage

gIDR(x, mu, sigma, rho, p, eps = 0.001, max.ite = 30)

Arguments

x	Numeric matrix with rows representing the number of omic features and columns representing the number of sample replicates. The numeric values must be positive and represent significance (not necessarily p-values).
mu	Starting value for the mean of the reproducible component. Numeric.
sigma	Starting value for the standard deviation of the reproducible component.
rho	Starting value for the correlation coefficient of the reproducible component.
p	Starting value for the proportion of the reproducible component.
eps	Stopping criterion. Iterations stop when the increment of the log-likelihood is less than eps times the log-likelihood. Default is 0.001.
max.ite	Maximum number of iterations. Default is 30.

Value

Returns a list of three elements:

idr

A numeric vector of the local IDR (Irreproducible Discovery Rate) for each observation (i.e., estimated conditional probability for each observation to belong to the irreproducible component).

IDR

A numerical vector of the expected Irreproducible Discovery Rate for observations that are as irreproducible or more irreproducible than the given observations.

est_param

Estimated parameters: p, rho, mu, sigma.

References

Q. Li, J. B. Brown, H. Huang, and P. J. Bickel. (2011)

Examples

# 1. Show that gIDR reduces to classical IDR for n=2.

# Load required packages.
library(idr)
library(eCV)

# Set seed for RNG.
set.seed(42)

# Simulate data.
out <- simulate_data(scenario = 2, n_features = 1e3)

# Set initial parameter values.
mu <- 2
sigma <- 1.3
rho <- 0.8
p <- 0.7

# Compare IDR and gIDR
idr.out <- est.IDR(x = out$sim_data, mu, sigma, rho, p)
gidr.out <- gIDR(x = out$sim_data, mu, sigma, rho, p)

# Show the results are the same.
all.equal(gidr.out$est_param, idr.out$para)



library(tidyverse)
# Plot results.
out$sim_data %>% as.data.frame() %>% 
mutate(idr = gidr.out$idr) %>%
ggplot(aes(x=`Rep 1`,y=`Rep 2`,color=idr)) +
 geom_point(size=1) + 
 scale_color_gradientn(colors=c("#F4364C", "#D5DADD", "#009CA6" ))+ 
 theme_classic()

#2. Show gIDR for n=10.

out <- simulate_data(scenario = 1, n_reps = 10, n_features = 1e3)
gidr.out <- gIDR(x = out$sim_data, mu, sigma, rho, p)
out$sim_data %>% as.data.frame() %>% 
mutate(idr = gidr.out$IDR) %>%
ggplot(aes(x = `Rep 1`, y = `Rep 2`, color = idr)) +
 geom_point(size = 1) + 
 scale_color_gradientn(colors=c("#F4364C", "#D5DADD", "#009CA6" ))+ 
 theme_classic()

eCV documentation built on May 29, 2024, 8:59 a.m.