PAGWAS (version 2.0)

Pathway Analysis Methods for Genomewide Association Data

Description

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.

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Version

Install

install.packages('PAGWAS')

Monthly Downloads

109

Version

2.0

License

GPL (>= 2)

Maintainer

Marina Evangelou

Last Published

December 8th, 2015

Functions in PAGWAS (2.0)

SNAL.calculation

Sparse Normal/Adaptive lasso method for finding associated variables. The SNAL method is applied to the linear regression Y= Phi beta + epsilon

pathways

A list of 2 pathways with their gene members

PAGWAS-package

Pathway Analysis Methods for Genomewide Association Data

NBF

Normal/Bayes factors method for finding associated pathways

genotypes

Genotypes for 100 SNPs and 75 individuals

snps.to.pathways

Assigns SNPs to pathways

FM.chi.pvalue

Calculates the Fisher's method p-value for each tested pathway

SNAL

Sparse Normal/Adaptive lasso method for finding associated pathways

snps.to.genes

Assigns SNPs to genes

create.pathway.df

Creates a pathway data frame

genes

A data frame of 20 artificial genes with their chromosomes and positions on the genome

SNPs

A data frame of 100 artificial SNPs with their chromosomes and positions on the genome