Searcharxiv⌕ Search

arXiv subjects

Marianne A. Jonker

Publications and source records attributed to Marianne A. Jonker.

3 recordsLinked to original sources

Bayesian Federated Inference for estimating Statistical Models based on Non-shared Multicenter Data sets

Identifying predictive factors for an outcome of interest via a multivariable analysis is often difficult when the data set is small. Combining data from different medical centers into a single (larger) database would alleviate this problem, but is in practice challenging due to regulatory and logistic problems. Federated Learning (FL) is a machine learning approach that aims to construct from local inferences in separate data centers what would have been inferred had the data sets been merged. It seeks to harvest the statistical power of larger data sets without actually creating them. The FL strategy is not always efficient and precise. Therefore, in this paper we refine and implement an alternative Bayesian Federated Inference (BFI) framework for multicenter data with the same aim as FL. The BFI framework is designed to cope with small data sets by inferring locally not only the optimal parameter values, but also additional features of the posterior parameter distribution, capturing information beyond what is used in FL. BFI has the additional benefit that a single inference cycle across the centers is sufficient, whereas FL needs multiple cycles. We quantify the performance of the proposed methodology on simulated and real life data.

stat.AP↗

A powerful MAF-neutral allele-based test for case-control association studies

In a case-control study aimed at locating autosomal disease variants for a disease of interest, association between markers and the disease status is often tested by comparing the marker minor allele frequencies (MAFs) between cases and controls. For most common allele-based tests the statistical power is highly dependent on the actual values of these MAFs, where associated markers with low MAFs have less power to be detected compared to associated markers with high MAFs. Therefore, the popular strategy of selecting markers for follow-up studies based primarily on their p-values is likely to preferentially select markers with high MAFs. We propose a new test which does not favor markers with high MAFs and improves the power for markers with low to moderate MAFs without sacrificing performance for markers with high MAFs and is therefore superior to most existing tests in this regard. An explicit formula for the asymptotic power function of the proposed test is derived theoretically, which allows for fast and easy computation of the corresponding p-values. The performance of the proposed test is compared with several existing tests both in the asymptotic and the finite sample size settings.

stat.AP↗

Detecting SNPs with interactive effects on a quantitative trait

Here we propose a test to detect effects of single nucleotide polymorphisms (SNPs) on a quantitative trait. Significant SNP-SNP interactions are more difficult to detect than significant SNPs, partly due to the massive amount of SNP-SNP combinations. We propose to move away from testing interaction terms, and move towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, we split the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in distribution between some individuals in one group and all other individuals, it possibly has an interactive effect. We propose a mixture test to detect both types of effects. Implicitly, the membership probabilities may suggest potential interacting variables. Analysing simulated and experimental data, we show that the proposed test is statistically powerful, maintains the type I error rate, and detects meaningful signals. The R package semisup is available from Bioconductor.

stat.ME↗