PAGWAS: Pathway Analysis Methods for Genomewide Association Data

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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.

Author
Marina Evangelou
Date of publication
2015-12-08 14:53:45
Maintainer
Marina Evangelou <m.evangelou@ic.ac.uk>
License
GPL (>= 2)
Version
2.0

View on CRAN

Man pages

create.pathway.df
Creates a pathway data frame
FM.chi.pvalue
Calculates the Fisher's method p-value for each tested...
genes
A data frame of 20 artificial genes with their chromosomes...
genotypes
Genotypes for 100 SNPs and 75 individuals
NBF
Normal/Bayes factors method for finding associated pathways
PAGWAS-package
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...
SNAL.calculation
Sparse Normal/Adaptive lasso method for finding associated...
SNPs
A data frame of 100 artificial SNPs with their chromosomes...
snps.to.genes
Assigns SNPs to genes
snps.to.pathways
Assigns SNPs to pathways

Files in this package

PAGWAS
PAGWAS/NAMESPACE
PAGWAS/data
PAGWAS/data/SNPs.rda
PAGWAS/data/genes.rda
PAGWAS/data/genotypes.rda
PAGWAS/data/pathways.rda
PAGWAS/R
PAGWAS/R/matrix.inv.calculation.R
PAGWAS/R/lars.calculation.R
PAGWAS/R/snps.to.genes.R
PAGWAS/R/NBF.R
PAGWAS/R/snps.to.pathways.R
PAGWAS/R/SNAL.calculation.R
PAGWAS/R/logproby.R
PAGWAS/R/SNAL.R
PAGWAS/R/create.pathway.df.R
PAGWAS/R/FM.chi.pvalue.R
PAGWAS/R/matrix.invroot.calculation.R
PAGWAS/MD5
PAGWAS/DESCRIPTION
PAGWAS/man
PAGWAS/man/FM.chi.pvalue.Rd
PAGWAS/man/pathways.Rd
PAGWAS/man/SNAL.Rd
PAGWAS/man/PAGWAS-package.Rd
PAGWAS/man/snps.to.genes.Rd
PAGWAS/man/SNPs.Rd
PAGWAS/man/genotypes.Rd
PAGWAS/man/genes.Rd
PAGWAS/man/SNAL.calculation.Rd
PAGWAS/man/create.pathway.df.Rd
PAGWAS/man/NBF.Rd
PAGWAS/man/snps.to.pathways.Rd