Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ordinalgmifs: An R Package for Ordinal Regression in High-dimensional Data Settings.

ABSTRACT: High-throughput genomic assays are performed using tissue samples with the goal of classifying the samples as normal < pre-malignant < malignant or by stage of cancer using a small set of molecular features. In such cases, molecular features monotonically associated with the ordinal response may be important to disease development; that is, an increase in the phenotypic level (stage of cancer) may be mechanistically linked through a monotonic association with gene expression or methylation levels. Though traditional ordinal response modeling methods exist, they assume independence among the predictor variables and require the number of samples (n) to exceed the number of covariates (P) included in the model. In this paper, we describe our ordinalgmifs R package, available from the Comprehensive R Archive Network, which can fit a variety of ordinal response models when the number of predictors (P) exceeds the sample size (n). R code illustrating usage is also provided.

SUBMITTER: Archer KJ

PROVIDER: S-EPMC4266195 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

ordinalgmifs: An R Package for Ordinal Regression in High-dimensional Data Settings.

Archer Kellie J KJ Hou Jiayi J Zhou Qing Q Ferber Kyle K Layne John G JG Gentry Amanda E AE

Cancer informatics 20141210

High-throughput genomic assays are performed using tissue samples with the goal of classifying the samples as normal < pre-malignant < malignant or by stage of cancer using a small set of molecular features. In such cases, molecular features monotonically associated with the ordinal response may be important to disease development; that is, an increase in the phenotypic level (stage of cancer) may be mechanistically linked through a monotonic association with gene expression or methylation level ...[more]

PMID: 25574124

Similar Datasets

Penalized logistic regression with low prevalence exposures beyond high dimensional settings.

Project description:Estimating and selecting risk factors with extremely low prevalences of exposure for a binary outcome is a challenge because classical standard techniques, markedly logistic regression, often fail to provide meaningful results in such settings. While penalized regression methods are widely used in high-dimensional settings, we were able to show their usefulness in low-dimensional settings as well. Specifically, we demonstrate that Firth correction, ridge, the lasso and boosting all improve the estimation for low-prevalence risk factors. While the methods themselves are well-established, comparison studies are needed to assess their potential benefits in this context. This is done here using the dataset of a large unmatched case-control study from France (2005-2008) about the relationship between prescription medicines and road traffic accidents and an accompanying simulation study. Results show that the estimation of risk factors with prevalences below 0.1% can be drastically improved by using Firth correction and boosting in particular, especially for ultra-low prevalences. When a moderate number of low prevalence exposures is available, we recommend the use of penalized techniques.

| S-EPMC6527211 | biostudies-literature

Regularization method for predicting an ordinal response using longitudinal high-dimensional genomic data.

Project description:Abstract An ordinal scale is commonly used to measure health status and disease related outcomes in hospital settings as well as in translational medical research. In addition, repeated measurements are common in clinical practice for tracking and monitoring the progression of complex diseases. Classical methodology based on statistical inference, in particular, ordinal modeling has contributed to the analysis of data in which the response categories are ordered and the number of covariates (p) remains smaller than the sample size (n). With the emergence of genomic technologies being increasingly applied for more accurate diagnosis and prognosis, high-dimensional data where the number of covariates (p) is much larger than the number of samples (n), are generated. To meet the emerging needs, we introduce our proposed model which is a two-stage algorithm: Extend the generalized monotone incremental forward stagewise (GMIFS) method to the cumulative logit ordinal model; and combine the GMIFS procedure with the classical mixed-effects model for classifying disease status in disease progression along with time. We demonstrate the efficiency and accuracy of the proposed models in classification using a time-course microarray dataset collected from the Inflammation and the Host Response to Injury study.

| S-EPMC4454613 | biostudies-literature

Regression analysis of correlated ordinal data using orthogonalized residuals.

Project description:Semi-parametric regression models for the joint estimation of marginal mean and within-cluster pairwise association parameters are used in a variety of settings for population-averaged modeling of multivariate categorical outcomes. Recently, a formulation of alternating logistic regressions based on orthogonalized, marginal residuals has been introduced for correlated binary data. Unlike the original procedure based on conditional residuals, its covariance estimator is invariant to the ordering of observations within clusters. In this article, the orthogonalized residuals method is extended to model correlated ordinal data with a global odds ratio, and shown in a simulation study to be more efficient and less biased with regards to estimating within-cluster association parameters than an existing extension to ordinal data of alternating logistic regressions based on conditional residuals. Orthogonalized residuals are used to estimate a model for three correlated ordinal outcomes measured repeatedly in a longitudinal clinical trial of an intervention to improve recovery of patients' perception of altered sensation following jaw surgery.

| S-EPMC4472482 | biostudies-literature

GLOBALLY ADAPTIVE QUANTILE REGRESSION WITH ULTRA-HIGH DIMENSIONAL DATA.

Project description:Quantile regression has become a valuable tool to analyze heterogeneous covaraite-response associations that are often encountered in practice. The development of quantile regression methodology for high dimensional covariates primarily focuses on examination of model sparsity at a single or multiple quantile levels, which are typically prespecified ad hoc by the users. The resulting models may be sensitive to the specific choices of the quantile levels, leading to difficulties in interpretation and erosion of confidence in the results. In this article, we propose a new penalization framework for quantile regression in the high dimensional setting. We employ adaptive L1 penalties, and more importantly, propose a uniform selector of the tuning parameter for a set of quantile levels to avoid some of the potential problems with model selection at individual quantile levels. Our proposed approach achieves consistent shrinkage of regression quantile estimates across a continuous range of quantiles levels, enhancing the flexibility and robustness of the existing penalized quantile regression methods. Our theoretical results include the oracle rate of uniform convergence and weak convergence of the parameter estimators. We also use numerical studies to confirm our theoretical findings and illustrate the practical utility of our proposal.

| S-EPMC4654965 | biostudies-literature

Obtaining insights from high-dimensional data: sparse principal covariates regression.

Project description:BACKGROUND:Data analysis methods are usually subdivided in two distinct classes: There are methods for prediction and there are methods for exploration. In practice, however, there often is a need to learn from the data in both ways. For example, when predicting the antibody titers a few weeks after vaccination on the basis of genomewide mRNA transcription rates, also mechanistic insights about the effect of vaccinations on the immune system are sought. Principal covariates regression (PCovR) is a method that combines both purposes. Yet, it misses insightful representations of the data as these include all the variables. RESULTS:Here, we propose a sparse extension of principal covariates regression such that the resulting solutions are based on an automatically selected subset of the variables. Our method is shown to outperform competing methods like sparse principal components regression and sparse partial least squares in a simulation study. Furthermore good performance of the method is illustrated on publicly available data including antibody titers and genomewide transcription rates for subjects vaccinated against the flu: the selected genes by sparse PCovR are higly enriched for immune related terms and the method predicts the titers for an independent test sample well. In comparison, no significantly enriched terms were found for the genes selected by sparse partial least squares and out-of-sample prediction was worse. CONCLUSIONS:Sparse principal covariates regression is a promising and competitive tool for obtaining insights from high-dimensional data. AVAILABILITY:The source code implementing our proposed method is available from GitHub, together with all scripts used to extract, pre-process, analyze, and post-process the data: https://github.com/katrijnvandeun/SPCovR .

| S-EPMC5870402 | biostudies-literature

The joint lasso: high-dimensional regression for group structured data.

Project description:We consider high-dimensional regression over subgroups of observations. Our work is motivated by biomedical problems, where subsets of samples, representing for example disease subtypes, may differ with respect to underlying regression models. In the high-dimensional setting, estimating a different model for each subgroup is challenging due to limited sample sizes. Focusing on the case in which subgroup-specific models may be expected to be similar but not necessarily identical, we treat subgroups as related problem instances and jointly estimate subgroup-specific regression coefficients. This is done in a penalized framework, combining an $\ell_1$ term with an additional term that penalizes differences between subgroup-specific coefficients. This gives solutions that are globally sparse but that allow information-sharing between the subgroups. We present algorithms for estimation and empirical results on simulated data and using Alzheimer's disease, amyotrophic lateral sclerosis, and cancer datasets. These examples demonstrate the gains joint estimation can offer in prediction as well as in providing subgroup-specific sparsity patterns.

| S-EPMC7868060 | biostudies-literature

Ordinal regression models for zero-inflated and/or over-dispersed count data.

Project description:Count data commonly arise in natural sciences but adequately modeling these data is challenging due to zero-inflation and over-dispersion. While multiple parametric modeling approaches have been proposed, unfortunately there is no consensus regarding how to choose the best model. In this article, we propose a ordinal regression model (MN) as a default model for count data given that this model is shown to fit well data that arise from several types of discrete distributions. We extend this model to allow for automatic model selection (MN-MS) and show that the MN-MS model generates superior inference when compared to using the full model or more traditional model selection approaches. The MN-MS model is used to determine how human biting rate of mosquitoes, known to be able to transmit malaria, are influenced by environmental factors in the Peruvian Amazon. The MN-MS model had one of the best fit and out-of-sample predictive skill amongst all models. While A. darlingi is strongly associated with highly anthropized landscapes, all the other mosquito species had higher mean biting rates in landscapes with a lower fraction of exposed soil and urban area, revealing a striking shift in species composition. We believe that the MN and MN-MS models are valuable additions to the modelling toolkit employed by environmental modelers and quantitative ecologists.

| S-EPMC6395857 | biostudies-other

NETWORK-REGULARIZED HIGH-DIMENSIONAL COX REGRESSION FOR ANALYSIS OF GENOMIC DATA.

Project description:We consider estimation and variable selection in high-dimensional Cox regression when a prior knowledge of the relationships among the covariates, described by a network or graph, is available. A limitation of the existing methodology for survival analysis with high-dimensional genomic data is that a wealth of structural information about many biological processes, such as regulatory networks and pathways, has often been ignored. In order to incorporate such prior network information into the analysis of genomic data, we propose a network-based regularization method for high-dimensional Cox regression; it uses an ℓ1-penalty to induce sparsity of the regression coefficients and a quadratic Laplacian penalty to encourage smoothness between the coefficients of neighboring variables on a given network. The proposed method is implemented by an efficient coordinate descent algorithm. In the setting where the dimensionality p can grow exponentially fast with the sample size n, we establish model selection consistency and estimation bounds for the proposed estimators. The theoretical results provide insights into the gain from taking into account the network structural information. Extensive simulation studies indicate that our method outperforms Lasso and elastic net in terms of variable selection accuracy and stability. We apply our method to a breast cancer gene expression study and identify several biologically plausible subnetworks and pathways that are associated with breast cancer distant metastasis.

| S-EPMC4549005 | biostudies-literature

High-dimensional variable selection for ordinal outcomes with error control.

Project description:Many high-throughput genomic applications involve a large set of potential covariates and a response which is frequently measured on an ordinal scale, and it is crucial to identify which variables are truly associated with the response. Effectively controlling the false discovery rate (FDR) without sacrificing power has been a major challenge in variable selection research. This study reviews two existing variable selection frameworks, model-X knockoffs and a modified version of reference distribution variable selection (RDVS), both of which utilize artificial variables as benchmarks for decision making. Model-X knockoffs constructs a 'knockoff' variable for each covariate to mimic the covariance structure, while RDVS generates only one null variable and forms a reference distribution by performing multiple runs of model fitting. Herein, we describe how different importance measures for ordinal responses can be constructed that fit into these two selection frameworks, using either penalized regression or machine learning techniques. We compared these measures in terms of the FDR and power using simulated data. Moreover, we applied these two frameworks to high-throughput methylation data for identifying features associated with the progression from normal liver tissue to hepatocellular carcinoma to further compare and contrast their performances.

| S-EPMC7820886 | biostudies-literature

HIGH DIMENSIONAL CENSORED QUANTILE REGRESSION.

Project description:Censored quantile regression (CQR) has emerged as a useful regression tool for survival analysis. Some commonly used CQR methods can be characterized by stochastic integral-based estimating equations in a sequential manner across quantile levels. In this paper, we analyze CQR in a high dimensional setting where the regression functions over a continuum of quantile levels are of interest. We propose a two-step penalization procedure, which accommodates stochastic integral based estimating equations and address the challenges due to the recursive nature of the procedure. We establish the uniform convergence rates for the proposed estimators, and investigate the properties on weak convergence and variable selection. We conduct numerical studies to confirm our theoretical findings and illustrate the practical utility of our proposals.

| S-EPMC6193274 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data