Resampling Collapsed Null Distributions for Simultaneous Inference

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Documentation for package ‘reconsi’ version 1.21.0

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binStats Bin the test statistic into equally sized bins
calcWeights Obtain weights as posterior probabilities to calculate the consensus null
estNormal Fast estimation of mean and standard deviation of a normal distrbution, optionally with weights
estP0 Estimate the fraction of true null hypotheses.
getApproxCovar Obtain a null covariance matrix of binned test statistics
getC1prop Find the dependence pat C1 of the approximate covariance matrix, and extract the ratio of the first eigenvalue to the sum of all positive eigenvalues
getFdr Calculate tail-area (Fdr) and local (fdr) false discovery rates, based on a certain null distribution
getG0 Obtain the consensus null
getTestStats A function to calculate observed and permuation z-statistics on a n-by-p matrix of observations
getTstat A function to obtain a t-test statistic efficiently. For internal use only
plotApproxCovar Plot an approximation of the correlation structure of the test statistics
plotCovar Plot an the corvariance matrix of the test statistics estimated through permutations
plotNull Plot the obtained null distribution along with a histogram of observed test statistics
ptEdit A custom function to calculate the distribution function of the t-test statistic. For internal use only
qtEdit A custom function to calculate the quantile function of the t-test statistic. For internal use only
quantCorrect Correct quantiles by not returning 0 or 1
reconsi Perform simultaneous inference through collapsed resampling null distributions
rowMultiply A function to efficiently row multiply a a-by-b matrix by a vector of length b. More memory intensive but that does not matter with given matrix sizes
stabExp A function to numerically stabilize an exponentiation. For internal use only
testDAA A function to test for differential absolute abundance on a phyloseq object
testDAA-method A function to test for differential absolute abundance on a phyloseq object
Vandeputte Microbiomes of Crohn's disease patients and healthy controls