Package: HDMT 1.0.5

James Dai

HDMT: A Multiple Testing Procedure for High-Dimensional Mediation Hypotheses

A multiple-testing procedure for high-dimensional mediation hypotheses. Mediation analysis is of rising interest in epidemiology and clinical trials. Among existing methods for mediation analyses, the popular joint significance (JS) test yields an overly conservative type I error rate and therefore low power. In the R package 'HDMT' we implement a multiple-testing procedure that accurately controls the family-wise error rate (FWER) and the false discovery rate (FDR) when using JS for testing high-dimensional mediation hypotheses. The core of our procedure is based on estimating the proportions of three component null hypotheses and deriving the corresponding mixture distribution of null p-values. Results of the data examples include better-behaved quantile-quantile plots and improved detection of novel mediation relationships on the role of DNA methylation in genetic regulation of gene expression. With increasing interest in mediation by molecular intermediaries such as gene expression, the proposed method addresses an unmet methodological challenge. Methods used in the package refer to James Y. Dai, Janet L. Stanford & Michael LeBlanc (2020) <doi:10.1080/01621459.2020.1765785>.

Authors:James Dai [aut, cre], Xiaoyu Wang [aut]

HDMT_1.0.5.tar.gz
HDMT_1.0.5.tar.gz(r-4.5-noble)HDMT_1.0.5.tar.gz(r-4.4-noble)
HDMT_1.0.5.tgz(r-4.4-emscripten)HDMT_1.0.5.tgz(r-4.3-emscripten)
HDMT.pdf |HDMT.html
HDMT/json (API)

# Install 'HDMT' in R:
install.packages('HDMT', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • exercise_input - An example dataset to demonstrate the usage of 'HDMT'
  • snp_input - An example dataset to demonstrate the usage of 'HDMT'

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.86 score 2 packages 12 scripts 298 downloads 5 exports 35 dependencies

Last updated 3 years agofrom:c142c822ca. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 26 2024
R-4.5-linuxOKNov 26 2024

Exports:adjust_quantilecorrect_qqplotfdr_estfwer_estnull_estimation

Dependencies:clicolorspacefansifarverfdrtoolggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrqvalueR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr

HDMT

Rendered fromHDMT.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2022-01-29
Started: 2022-01-29