FM.chi.pvalue           Calculates the Fisher's method p-value for each
                        tested pathway
NBF                     Normal/Bayes factors (NBF) method for finding
                        associated pathways
PAGWAS-package          Pathway analysis methods for genomewide
                        association data
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
create.pathway.matrix   Creates a pathway matrix
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
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
snps.to.genes           Assigns SNPs to genes according to their
                        physical distance
snps.to.pathways        Assigns SNPs to pathways
