1,228 research outputs found
Penalized EM algorithm and copula skeptic graphical models for inferring networks for mixed variables
In this article, we consider the problem of reconstructing networks for
continuous, binary, count and discrete ordinal variables by estimating sparse
precision matrix in Gaussian copula graphical models. We propose two
approaches: penalized extended rank likelihood with Monte Carlo
Expectation-Maximization algorithm (copula EM glasso) and copula skeptic with
pair-wise copula estimation for copula Gaussian graphical models. The proposed
approaches help to infer networks arising from nonnormal and mixed variables.
We demonstrate the performance of our methods through simulation studies and
analysis of breast cancer genomic and clinical data and maize genetics data
Multiple Imputation Using Gaussian Copulas
Missing observations are pervasive throughout empirical research, especially
in the social sciences. Despite multiple approaches to dealing adequately with
missing data, many scholars still fail to address this vital issue. In this
paper, we present a simple-to-use method for generating multiple imputations
using a Gaussian copula. The Gaussian copula for multiple imputation (Hoff,
2007) allows scholars to attain estimation results that have good coverage and
small bias. The use of copulas to model the dependence among variables will
enable researchers to construct valid joint distributions of the data, even
without knowledge of the actual underlying marginal distributions. Multiple
imputations are then generated by drawing observations from the resulting
posterior joint distribution and replacing the missing values. Using simulated
and observational data from published social science research, we compare
imputation via Gaussian copulas with two other widely used imputation methods:
MICE and Amelia II. Our results suggest that the Gaussian copula approach has a
slightly smaller bias, higher coverage rates, and narrower confidence intervals
compared to the other methods. This is especially true when the variables with
missing data are not normally distributed. These results, combined with
theoretical guarantees and ease-of-use suggest that the approach examined
provides an attractive alternative for applied researchers undertaking multiple
imputations
netgwas: An R Package for Network-Based Genome-Wide Association Studies
Graphical models are powerful tools for modeling and making statistical
inferences regarding complex associations among variables in multivariate data.
In this paper we introduce the R package netgwas, which is designed based on
undirected graphical models to accomplish three important and interrelated
goals in genetics: constructing linkage map, reconstructing linkage
disequilibrium (LD) networks from multi-loci genotype data, and detecting
high-dimensional genotype-phenotype networks. The netgwas package deals with
species with any chromosome copy number in a unified way, unlike other
software. It implements recent improvements in both linkage map construction
(Behrouzi and Wit, 2018), and reconstructing conditional independence network
for non-Gaussian continuous data, discrete data, and mixed
discrete-and-continuous data (Behrouzi and Wit, 2017). Such datasets routinely
occur in genetics and genomics such as genotype data, and genotype-phenotype
data. We demonstrate the value of our package functionality by applying it to
various multivariate example datasets taken from the literature. We show, in
particular, that our package allows a more realistic analysis of data, as it
adjusts for the effect of all other variables while performing pairwise
associations. This feature controls for spurious associations between variables
that can arise from classical multiple testing approach. This paper includes a
brief overview of the statistical methods which have been implemented in the
package. The main body of the paper explains how to use the package. The
package uses a parallelization strategy on multi-core processors to speed-up
computations for large datasets. In addition, it contains several functions for
simulation and visualization. The netgwas package is freely available at
https://cran.r-project.org/web/packages/netgwasComment: 32 pages, 9 figures; due to the limitation "The abstract field cannot
be longer than 1,920 characters", the abstract appearing here is slightly
shorter than that in the PDF fil
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