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Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies

Figure 2

Evaluation of PANAMA and alternative methods on the simulated eQTL dataset.

(a,b) number of recovered cis and trans associations as a function of the chosen false discovery rate cutoff. To circumvent biases due to linkage, at most one association per chromosome and gene is counted. (c) Receiver Operating Characteristics (ROC) for recovering true simulated associations, depicting the true positive rate (TPR) as a function of the permitted false positive rate (FPR). (d) inflation factors, defined as , indicating either inflated p-value distributions () or deflation () of the respective tests statistics. (e) Area under the ROC curve for alternative simulated datasets, subsampling certain fractions of number of simulated trans association. (f) Area under the ROC curve for alternative simulated datasets, subsampling the number of simulated confounding factors.

Figure 2

doi: https://doi.org/10.1371/journal.pcbi.1002330.g002