Package: PAGWAS 2.0

PAGWAS: Pathway Analysis Methods for Genomewide Association Data

Bayesian hierarchical methods for pathway analysis of genomewide association data: Normal/Bayes factors and Sparse Normal/Adaptive lasso. The Frequentist Fisher's product method is included as well.

Authors:Marina Evangelou

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PAGWAS.pdf |PAGWAS.html✨
PAGWAS/json (API)

# Install 'PAGWAS' in R:
install.packages('PAGWAS', repos = c('https://mevangelou.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • SNPs - A data frame of 100 artificial SNPs with their chromosomes and positions on the genome
  • genes - A data frame of 20 artificial genes with their chromosomes and positions on the genome
  • genotypes - Genotypes for 100 SNPs and 75 individuals
  • list.of.parameters - A list with possible hyper-parameters for NBF
  • pathways - A list of 2 pathways with their gene members

On CRAN:

Conda-Forge:

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

1.04 score 11 scripts 154 downloads 7 exports 5 dependencies

Last updated 9 years agofrom:f72f5ebcca. Checks:1 OK, 7 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 24 2025
R-4.5-winERRORFeb 24 2025
R-4.5-macERRORFeb 24 2025
R-4.5-linuxERRORFeb 24 2025
R-4.4-winERRORFeb 24 2025
R-4.4-macERRORFeb 24 2025
R-4.3-winERRORFeb 24 2025
R-4.3-macERRORFeb 24 2025

Exports:create.pathway.dfFM.chi.pvalueNBFSNALSNAL.calculationsnps.to.genessnps.to.pathways

Dependencies:codetoolsforeachiteratorslarsmnormt