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keywords: htest
title: Cochran's C test of homogeneity of variances
description: Performs a Cochran's test of the null hypothesis that the largest variance in several sampled variances are the same.

keywords: htest
title: Student-Newman-Keuls (SNK) procedure
description: This function perforns a SNK post-hoc test of means on the factors of a chosen term of the model, comparing among levels of one factor within each level of other factor or combination of factors.

keywords: htest
title: Proportion of the variables under the null hypothesis
description: Estimate of the proportion of the variables under the null hypothesis using tail posterior probabilities

keywords: htest
title: FDR for tail posterior probability
description: Calculate the false discovery rate (FDR) for the tail posterior probability

keywords: htest
title: Estimate the FDR (false discovery rate) and related quantities for BGmix output.
description: Given a threshold on the posterior probabilities, genes are declared as null or differentially expressed. For any given threshold, the FDR (false discovery rate) and FNR (false non-discovery rate) can be estimated using the posterior probabilities. Estimated numbers of false positives and false negatives are also output.

keywords: htest
title: Tail posterior probability for BGmix output.
description: For differential expression models with unstructured priors (no mixture prior), calculates tail posterior probabality and FDR, and plots a histogram. Uses whole posterior distributions of likelihood parameters (found by 'ccTrace') and posterior means of hyperparameters (found by 'ccParams').

keywords: htest
title: Modify binary sequential boundary
description: Modify several different aspects of a binary sequential boundary. Most modifications do not change the stopping boundaries. The exceptions are 'missN', which allows modifications for missing assessments, and 'closeout', which allows for early stopping of the trial for administrative reasons (i.e., reasons that do not depend on the responses in the trial). Other modifications possible: level of the confidence intervals (using tsalpha, conf.level, or alternative), which boundaries are binding (i.e., can change from a boundary with binding futility boundaries to one with non-binding futility boundaries), null hypothesis value (theta0), and whether the confidence intervals should match the non-binding futility p-values on the superiority boundaries (cipMatch).

keywords: htest
title: The maxT procedure for order restricted inference
description: The function calculates the adjusted p-values for the five test statistics (the global likelihood test, Williams, Marcus, M, and the modified M) using the maxT procedure.

keywords: htest
title: Obtaining the delta table in the SAM procedure
description: The function obtains the delta table in the SAM procedure for the five test statistics (the global likelihood test, Williams, Marcus, M, and the modified M).

keywords: htest
title: The five SAM test statistics calculated for both the increasing and decreasing trends
description: The function calculates the values for the five SAM test statistics (the global likelihood test, Williams, Marcus, M, and the modified M) for the most likely direction.