Pathway analysis methods for genomewide association data

Documentation for package ‘PAGWAS’ version 1.0

PAGWAS-package	Pathway analysis methods for genomewide association data
create.pathway.matrix	Creates a pathway matrix
FM.chi.pvalue	Calculates the Fisher's method p-value for each tested pathway
genes	A data-frame of 20 genes with their chromosomes and positions on the genome
genotypes	Genotypes for 100 SNPs
list.of.parameters	A list with possible hyper-parameters for NBF
NBF	Normal/Bayes factors (NBF) method for finding associated pathways
PAGWAS	Pathway analysis methods for genomewide association data
pathways	A list of 2 pathways with their gene members
return.a.SNAL	Returns the hyper-parameter a of SNAL
return.bf.NBF	Returns the Bayes factor threshold of NBF
return.hyperparameters.NBF	Returns the four hyper-parameters of NBF
return.s2.SNAL	Returns the s2 tuning parameter of SNAL
roc.convex	Computes the area under a ROC curve
SNAL	Sparse Normal/Adaptive lasso (SNAL) method for finding associated pathways
SNPs	A data-frame of 100 SNPs with their chromosomes and positions on the genome
snps.to.genes	Assigns SNPs to genes according to their physical distance
snps.to.pathways	Assigns SNPs to pathways