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Calculates the Fisher's method p-value for a set of p-values. It returns both the p-value and the test statistic value of the Fisher's product method.
● Data Source:
CranContrib
● Keywords:
● Alias: FM.chi.pvalue
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SNAL
(Package: PAGWAS) :
Sparse Normal/Adaptive lasso method for finding associated pathways
Sparse Normal/Adaptive lasso method applied for finding the associated pathways. The iterative algorithm suggested by Wipf and Nagarajan (2008) is applied. A vector equal to the number of tested pathways is returned, the zero entries of the vector correspond to the pathways that are not associated. The posterior estimates of the beta coefficients are also returned as they are described by Wipf and Nagarajan (2008).
● Data Source:
CranContrib
● Keywords:
● Alias: SNAL
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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 method is included as well.
● Data Source:
CranContrib
● Keywords: package
● Alias: PAGWAS, PAGWAS-package
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Assigns SNPs to genes based on their physical distance.
● Data Source:
CranContrib
● Keywords:
● Alias: snps.to.genes
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For more details please read SNAL.
● Data Source:
CranContrib
● Keywords:
● Alias: SNAL.calculation
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Returns a data frame with L rows and M columns. L is the number of SNPs in the genotypes data frame and M is the number of tested pathways.
● Data Source:
CranContrib
● Keywords:
● Alias: create.pathway.df
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A vector of the computed Bayes factors for the tested pathways.
● Data Source:
CranContrib
● Keywords:
● Alias: NBF
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Assigns SNPs to pathways, using the pathway gene members and the SNPs assigned to each gene.
● Data Source:
CranContrib
● Keywords:
● Alias: snps.to.pathways
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providing 
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