Parmigiani, Giovanni; Chen, Sining; Velculescu, Victor E. TRAB: testing whether mutation frequencies are above an unknown background. (English) Zbl 1276.92072 Stat. Appl. Genet. Mol. Biol. 7, No. 1, Article No. 11, 8 p. (2008). Summary: To rigorously determine whether a gene or a set of genes have alterations that are involved in carcinogenesis requires a comparison of the prevalence of identified changes to a control mutation frequency present in tumor DNA. To facilitate this task, we develop a testing approach and the associated R library, called TRAB, that evaluates whether the frequency of somatic mutation in a given gene is higher than that observed in a control group of genes. Specifically, we test the null hypothesis that the frequency belongs to a control population of frequencies, against the alternative hypothesis that the frequency is higher. Mutation frequencies in the control group are themselves allowed to be variable. TRAB computes the a posteriori probability and the Bayes factor for the hypothesis using a hierarchical Bayesian approach. MSC: 92D10 Genetics and epigenetics 62P10 Applications of statistics to biology and medical sciences; meta analysis Keywords:hierarchical Bayesian models; mutation analysis Software:R; TRAB PDFBibTeX XMLCite \textit{G. Parmigiani} et al., Stat. Appl. Genet. Mol. Biol. 7, No. 1, Article No. 11, 8 p. (2008; Zbl 1276.92072) Full Text: DOI Link