| Type: | Package |
| Title: | Partial Correlation Graph with Information Incorporation |
| Version: | 1.1.2 |
| Description: | Large-scale gene expression studies allow gene network construction to uncover associations among genes. This package is developed for estimating and testing partial correlation graphs with prior information incorporated. |
| License: | MIT + file LICENSE |
| URL: | https://haowang47.github.io/PCGII/ |
| Depends: | R(≥ 4.3.0) |
| Imports: | stats, corpcor (≥ 1.6.10), glmnet, igraph (≥ 1.5.0.1), Matrix, dplyr (≥ 1.1.4) |
| Suggests: | mvtnorm, tidyverse, knitr, rmarkdown, testthat (≥ 3.0.0) |
| VignetteBuilder: | knitr |
| Config/testthat/edition: | 3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Language: | en-US |
| NeedsCompilation: | no |
| Packaged: | 2024-01-31 16:30:07 UTC; haowang |
| Author: | Hao Wang [aut, cre], Yumou Qiu [aut], Peng Liu [aut] |
| Maintainer: | Hao Wang <haydo.wang@outlook.com> |
| Repository: | CRAN |
| Date/Publication: | 2024-02-02 18:30:05 UTC |
Get the estimated partial correlation graph with information incorporation
Description
PCGII() is the function to apply the proposed method to get the estimated partial correlation graph with information incorporation. Remark: mathematical standardization will be automatically done within the function.
Usage
PCGII(df, prior, lambda)
Arguments
df |
The main expression dataset, an n by p matrix, 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. |
lambda |
The regularization parameter, used in the node-wise regression. If missing, default lambda will be used which is at the order of sqrt(2*log(p)/n). |
Value
A list. The list contains estimated partial correlation matrix (Est), sparse partial correlation estimation matrix with threshold (EstThresh), estimated kappa (kappa), estimated test statistics matrix of partial correlations (tscore), sample size (n) and number of nodes (p).
Examples
library(PCGII)
library(corpcor)
library(glmnet)
library(igraph)
library(Matrix)
library(mvtnorm)
# Simulating data
set.seed(1234567)
n=50 # sample size
p=30 # number of nodes
Omega=make_random_precision_mat(eta=.01, p=p)
# population covariance matrix, which is used to generate data
Sigma=solve(Omega)
# simulate expression data
X = rmvnorm(n = n, sigma = Sigma)
lam=2*sqrt(log(p)/n) ## fixed lambda
# directed prior network
prior_set=as.data.frame(matrix(data=c(5,6, 28,24), nrow=2, ncol=2, byrow = TRUE))
colnames(prior_set)=c("row", "col")
prior_set=undirected_prior(prior_set)
PCGII_out=PCGII(df=X, prior=prior_set, lambda = lam)
inference_out=inference(list=PCGII_out)
diag(inference_out)=0
net=graph_from_adjacency_matrix(inference_out, mode = "undirected")
plot(net, vertex.size=4,
vertex.label.dist=0.5,
vertex.color="red",
edge.arrow.size=0.5,
layout=layout_in_circle(net))
Get the estimated partial correlation graph without information incorporation
Description
clevel() is the function to apply the method originally proposed in paper "Qiu, Y., & Zhou, X. H. (2020). Estimating c-level partial correlation graphs with application to brain imaging". It is used to get the estimated partial correlation graph without information incorporation. Remark: mathematical standardization will be automatically done within the function.
Usage
clevel(df, lambda)
Arguments
df |
The main expression dataset, an n by p matrix, in which each row corresponds to a sample and each column represents expression/abundance of an omics feature. |
lambda |
The regularization parameter, used in the node-wise regression. If missing, default lambda will be used which is at the order of sqrt(2*log(p)/n). |
Value
A list. The list contains estimated partial correlation matrix (Est), sparse partial correlation estimation matrix with threshold (EstThresh), estimated kappa (kappa), estimated test statistics matrix of partial correlations (tscore), sample size (n) and number of nodes (p).
Examples
library(PCGII)
library(corpcor)
library(glmnet)
library(igraph)
library(Matrix)
library(mvtnorm)
# Simulating data
set.seed(1234567)
n=50 # sample size
p=30 # number of nodes
Omega=make_random_precision_mat(eta=.01, p=p)
# population covariance matrix, which is used to generate data
Sigma=solve(Omega)
# simulate expression data
X = rmvnorm(n = n, sigma = Sigma)
lam=2*sqrt(log(p)/n) ## fixed lambda
CLEVEL_out=clevel(df=X, lambda = lam)
inference_out=inference(list=CLEVEL_out)
diag(inference_out)=0
net=graph_from_adjacency_matrix(inference_out, mode = "undirected")
plot(net,
vertex.size=4,
vertex.label.dist=0.5,
vertex.color="red",
edge.arrow.size=0.5,
layout=layout_in_circle(net))
Conduct simultaneous inference of estimated partial correlations
Description
Inference() is the function to conduct simultaneous inference of estimated partial correlations.
Usage
inference(list, alpha = 0.05)
Arguments
list |
A list returned by either 'PCGII()' or 'clevel()'. |
alpha |
A pre-determined False Discovery Rate. Nominal FDR is set at 0.05 by default. |
Value
An adjacency matrix of significant partial correlations.
Examples
library(igraph)
library(PCGII)
library(mvtnorm)
# Simulating data
set.seed(1234567)
n=50 # sample size
p=30 # number of nodes
Omega=make_random_precision_mat(eta=.01, p=p)
# population covariance matrix, which is used to generate data
Sigma=solve(Omega)
# simulate expression data
X = rmvnorm(n = n, sigma = Sigma)
lam=2*sqrt(log(p)/n) ## fixed lambda
# directed prior network
prior_set=as.data.frame(matrix(data=c(5,6, 28,24), nrow=2, ncol=2, byrow = TRUE))
colnames(prior_set)=c("row", "col")
prior_set=undirected_prior(prior_set)
PCGII_out=PCGII(df=X, prior=prior_set, lambda = lam)
inference_out=inference(list=PCGII_out)
diag(inference_out)=0
net=graph_from_adjacency_matrix(inference_out, mode = "undirected")
plot(net, vertex.size=4,
vertex.label.dist=0.5,
vertex.color="red",
edge.arrow.size=0.5,
layout=layout_in_circle(net))
Generate block-diagonal matrix of size p by p
Description
A utility function generates block-diagonal matrix of size p by p with blocks B1, B2, ..., Bk. Each block matrix is of size blocksize by blocksize. The off-diagonal elements in block matrix are generated from uniform (min.beta, max.beta). The diagonal elements in block matrix are generated from uniform (1, 1.25).
Usage
makeBlockDiag(blocksize = 4, p = 20, min.beta = 0.3, max.beta = 0.9)
Arguments
blocksize |
A positive integer, the dimension of the block matrix. Note, 'blocksize' has to be a factor of 'p'. |
p |
A positive integer, the size of the block-diagonal matrix. |
min.beta |
A positive number, lower limits of the uniform distribution. |
max.beta |
A positive number, upper limits of the uniform distribution. |
Value
A block-diagonal matrix of size 'p' by 'p'.
Examples
mat = makeBlockDiag(blocksize=4, p=20)
Generate unstructured/random network skeleton and simulates corresponding precision matrix
Description
A utility function generates unstructured/random network skeleton and simulates corresponding precision matrix. The non-zero elements of the precision matrix are generated randomly from a uniform distribution with parameters (-upper, -lower) UNION (lower, upper).
Usage
make_random_precision_mat(
eta = 0.01,
p = 20,
lower = 0.2,
upper = 0.5,
diag = 0.1
)
Arguments
eta |
A number between 0 and 1, the probability for drawing an edge between two arbitrary vertices, i.e. the sparsity of the network. |
p |
A positive integer, the number of vertices. |
lower |
A positive number, lower limits of the uniform distribution. |
upper |
A positive number, upper limits of the uniform distribution. |
diag |
A small positive number to be added to diagonal elements, which guarantees the precision matrix is positive definite. |
Value
A precision matrix of size p by p.
Examples
Omega = make_random_precision_mat(eta=.2, p=10)
Generate scale-free network skeleton and simulates corresponding precision matrix
Description
A utility function generates scale-free network skeleton and simulates corresponding precision matrix. The non-zero elements of the precision matrix are generated randomly from a uniform distribution with parameters (-upper, -lower) UNION (lower, upper).
Usage
make_sf_precision_mat(
e = 1,
power = 1,
p = 20,
lower = 0.2,
upper = 0.5,
diag = 0.1
)
Arguments
e |
Numeric constant, the number of edges to add in each time step, see sample_pa(). |
power |
Numeric constant, the power of the preferential attachment for scale-free network, the default is 1, , see sample_pa(). |
p |
A positive integer, the number of vertices. |
lower |
A positive number, lower limits of the uniform distribution. |
upper |
A positive number, upper limits of the uniform distribution. |
diag |
A small positive number to be added to diagonal elements, which guarantees the precision matrix is positive definite. |
Value
A precision matrix of size p by p.
Examples
Omega = make_sf_precision_mat(e=1, p=10)
Utility function for PCGII inference results
Description
A utility function takes PCGII inference results as input and generates an adjacency matrix corresponding to the significant partial correlations
Usage
sigs2mat(sigs, P)
Arguments
sigs |
A dataframe of locations (row, col) of selected edges. |
P |
A number, the number of nodes in the network. |
Value
A matrix of size P*(P-1)/2, with 0, 1.
Examples
edges=cbind.data.frame(row=c(1,2,3,1,6,2,1,6,1,4),
col=c(2,1,1,3,2,6,6,1,4,1)) # five edges
sigs2mat(sigs = edges, P = 6)
Pre-process the input prior set to ensure the input prior set corresponds to an undirected prior network
Description
An utility function to pre-process the input prior set. This function will ensure the input prior set corresponds to an undirected prior network. If the prior network is believed to be directed, no pre-processing of the prior set is needed. Remark: this function is not necessary. Prior set should be considered carefully before running the network analysis. If the prior network connections are believed to be undirected while the prior set only includes one way connections for simplicity, this function will duplicate the connections and swap the direction automatically.
Usage
undirected_prior(prior)
Arguments
prior |
A k by 2 data.frame of prior set, in which each row corresponds to a pair of nodes (any omics features) that are connected under prior belief |
Value
A 2-column data.frame of pre-processed prior set, in which the connection between any pair of nodes is undirected.
Examples
prior=as.data.frame(matrix(c(1,2,1,5,1,10), ncol=2, byrow=TRUE))
## a prior set of 3 connections (1-2, 1-3, 1-10)
colnames(prior)=c("row", "col")
undirected=undirected_prior(prior)