PAGWAS: Pathway Analysis Methods for Genomewide Association Data
Version 2.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorMarina Evangelou
Date of publication2015-12-08 14:53:45
MaintainerMarina Evangelou <m.evangelou@ic.ac.uk>
LicenseGPL (>= 2)
Version2.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PAGWAS")

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

Functions

FM.chi.pvalue Man page Source code
NBF Man page Source code
PAGWAS Man page
PAGWAS-package Man page
SNAL Man page Source code
SNAL.calculation Man page Source code
SNPs Man page
create.pathway.df Man page Source code
genes Man page
genotypes Man page
lars.calculation Source code
logproby Source code
matrix.inv.calculation Source code
matrix.invroot.calculation Source code
pathways Man page
snps.to.genes Man page Source code
snps.to.pathways Man page Source code

Files

NAMESPACE
data
data/SNPs.rda
data/genes.rda
data/genotypes.rda
data/pathways.rda
R
R/matrix.inv.calculation.R
R/lars.calculation.R
R/snps.to.genes.R
R/NBF.R
R/snps.to.pathways.R
R/SNAL.calculation.R
R/logproby.R
R/SNAL.R
R/create.pathway.df.R
R/FM.chi.pvalue.R
R/matrix.invroot.calculation.R
MD5
DESCRIPTION
man
man/FM.chi.pvalue.Rd
man/pathways.Rd
man/SNAL.Rd
man/PAGWAS-package.Rd
man/snps.to.genes.Rd
man/SNPs.Rd
man/genotypes.Rd
man/genes.Rd
man/SNAL.calculation.Rd
man/create.pathway.df.Rd
man/NBF.Rd
man/snps.to.pathways.Rd
PAGWAS documentation built on May 20, 2017, 4:28 a.m.