Package: SMAHP 0.0.5

Weijia Fu

SMAHP: Survival Mediation Analysis of High-Dimensional Proteogenomic Data

SMAHP (pronounced as SOO-MAP) is a novel multi-omics framework for causal mediation analysis of high-dimensional proteogenomic data with survival outcomes. The full methodological details can be found in our recent preprint by Ahn S et al. (2025) <doi:10.48550/arXiv.2503.08606>.

Authors:Seungjun Ahn [aut], Weijia Fu [cre, aut], Zhigang Li [ctb]

SMAHP_0.0.5.tar.gz
SMAHP_0.0.5.tar.gz(r-4.5-noble)SMAHP_0.0.5.tar.gz(r-4.4-noble)
SMAHP_0.0.5.tgz(r-4.4-emscripten)SMAHP_0.0.5.tgz(r-4.3-emscripten)
SMAHP.pdf |SMAHP.html✨
SMAHP/json (API)

# Install 'SMAHP' in R:

install.packages('SMAHP', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

example_dat - Example Dataset

On CRAN:

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

2.00 score 10 exports 42 dependencies

Last updated 4 hours agofrom:92baeb3971. Checks:3 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 24 2025
R-4.5-linux	OK	Mar 24 2025
R-4.4-linux	OK	Mar 24 2025

Exports:get_adjusted_p get_coef get_pairs get_raw_p get_sig_pathway SIS_combo SMAHP StepOne StepThree StepTwo

Dependencies:cli codetools colorspace data.table fansi farver fdrtool foreach ggplot2 glmnet glue gtable irlba isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv munsell ncvreg nlme penAFT pillar pkgconfig R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang scales shape survival tibble utf8 vctrs viridisLite withr

SMAHP

Weijia Fu, Seungjun Ahn

Rendered fromSMAHP.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2025-03-24
Started: 2025-03-24

Citation

Readme and manuals

Help Manual

Help page	Topics
Example Dataset	example_dat
A function that returns adjusted p-values	get_adjusted_p
A function that extracts coefficients.	get_coef
A function that returns mediation-exposure matrix	get_pairs
A function that returns unadjusted p-values	get_raw_p
A function that returns significant pathways.	get_sig_pathway
SIS combo	SIS_combo
Main function	SMAHP
Penalized mediation and outcome models	StepOne
Post-hoc model	StepThree
Select M-X pairs via SIS	StepTwo