R: Pathway Analysis Methods for Genomewide Association Data

# Pathway Analysis Methods for Genomewide Association Data

## Documentation for package ‘PAGWAS’ version 2.0

- DESCRIPTION file.

## Help Pages

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