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PCGII License: MIT v3

R Package for Information-incorporated Gene Network Construction with FDR Control

Authors:

Hao Wang, Yumou Qiu and Peng Liu.

Contact:

[] (Hao Wang)

Citation:

Wang, H., Qiu, Y.*, Guo, H., Yin, Y., Liu, P.*, 2024. Information-incorporated Gene Network Construction with FDR Control. Under review.

Installation and Package loading 

> # R version is required >= 3.4.4
> # When the first time to use the package, please make sure dependent packages are installed under your R environment, if not, please use commands below to install
> # install.packages("tidyverse")
> # install.packages("glmnet")
> # install.packages("mvtnorm")
> # install.packages("igraph")
> # install.packages("Matrix")
> # Two ways to install PCGII
> #
> #
> # Option 1
> # install.packages("PCGII")
> # Option 2
> # install "devtools" package in your R environment
> # devtools::install_github("HaoWang47/PCGII")
> #
> #
> library(PCGII)
> library(corpcor)
> library(glmnet)
> library(igraph)
> library(Matrix)
> library(mvtnorm)
> library(tidyverse)

This is a tutorial script for researchers who are interested in applying PCGII on omics data to learn the direct association structure of omics features. The main function PGCII() takes a biologically pre-processed expression data matrix as input, and returns a list of statistics (estimates and test statistics). The function inference() takes a list returned by PGCII() as input and conduct simultaneous test to identify significant partial correlations with False Discovery Rate (FDR) controlled at a pre-determined nominal level (0.05 by default).

Usage

PCGII()

  • Input:
    • df: the main expression data, an n by p matrix/dataframe, in which each row corresponds to a sample and each column represents expression/abundance of an omics feature;
    • prior: the prior set, a k by 2 dataframe, in which each row corresponds to a pair of nodes (any omics features) that are connected under prior belief. Note, prior input has to be dataframe with column names “row” and “col”;
    • lambda: the regularization parameter, used in the node-wise regression. If missing, default lambda will be used which is at the order of sqrt(2log(p/sqrt(n))/n).
  • Remark: mathematical standardization will be automatically done within the function.
  • Output: This function returns a list of
    • Est: estimated partial correlation matrix;
    • EstThresh: sparse partial correlation estimation matrix with threshold;
    • kappa: estimated ratio of forth and squared second moment of residuals, please refer to the manuscript for details;
    • tscore: estimated test statistics matrix of partial correlations;
    • n: sample size;
    • p: number of genes under study.

Inference()

  • Input:
    • list: a list returned by either PCGII() or clevel().
    • alpha: pre-determined False Discovery Rate. Nominal FDR is set at 0.05 by default.
  • Output: an adjacency matrix of significant partial correlations.

Network Analysis

Simulate data X from a scale-free network g.

> # Simulating data
> set.seed(1234567)
> n=50 # sample size
> p=30 # number of nodes
>
> omega=make_random_precision_mat(eta=.01, p=p)
>
> Sigma=solve(omega) # population covariance matrix, which is used to generate data
> X = rmvnorm(n = n, sigma = Sigma) # simulate expression data

Network analysis of data matrix X.

> # determine tuning parameter: fixed lambda
> lam=2*sqrt(log(p)/n)
>
> # create prior set: directed prior network
> prior_set=matrix(data=c(6,5, 28,14), nrow=2, ncol=2, byrow = TRUE)
> colnames(prior_set)=c("row", "col")
> PCGII_out=PCGII(df=X, prior=as.data.frame(prior_set), lambda = lam)
> inference_out=inference(list=PCGII_out)
> diag(inference_out)=0
> # Visualization
> inference_out %>%
+   graph_from_adjacency_matrix(mode = "undirected") %>%
+   plot(vertex.size=4, vertex.label.dist=0.5, vertex.color="red", edge.arrow.size=0.5)
>
> # create prior set: undirected prior network
> PCGII_out=PCGII(df=X, prior=undirected_prior(prior_set), lambda = lam)
> inference_out=inference(list=PCGII_out)
> diag(inference_out)=0
> # Visualization
> inference_out %>%
+   graph_from_adjacency_matrix(mode = "undirected") %>%
+   plot(vertex.size=4, vertex.label.dist=0.5, vertex.color="red", edge.arrow.size=0.5)