Pathway Analysis Methods for Genomewide Association Data

Documentation for package ‘PAGWAS’ version 2.0

PAGWAS-package	Pathway Analysis Methods for Genomewide Association Data
create.pathway.df	Creates a pathway data frame
FM.chi.pvalue	Calculates the Fisher's method p-value for each tested pathway
genes	A data frame of 20 artificial genes with their chromosomes and positions on the genome
genotypes	Genotypes for 100 SNPs and 75 individuals
NBF	Normal/Bayes factors method for finding associated pathways
PAGWAS	Pathway Analysis Methods for Genomewide Association Data
pathways	A list of 2 pathways with their gene members
SNAL	Sparse Normal/Adaptive lasso method for finding associated pathways
SNAL.calculation	Sparse Normal/Adaptive lasso method for finding associated variables. The SNAL method is applied to the linear regression Y= Phi beta + epsilon
SNPs	A data frame of 100 artificial SNPs with their chromosomes and positions on the genome
snps.to.genes	Assigns SNPs to genes
snps.to.pathways	Assigns SNPs to pathways