R Graphical Manual

Last data update: 2014.03.03

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get_bh_threshold (Package: IHW) : Data-driven threshold of Benjamini Hochberg Procedure

Given pvalues and a nominal significance level alpha, this function returns the rejection threshold of the Benjamini-Hochberg procedure, i.e. a value t_BH such that p-values with P_i <= t_BH get rejected by the procedure.

● Data Source: BioConductor
● Keywords:
● Alias: get_bh_threshold
● 0 images

groups_by_filter (Package: IHW) : Stratify hypotheses based on increasing value of the covariate

Hypotheses are stratified into nbins different strata of (approximately) equal size based on increasing value of the covariate

● Data Source: BioConductor
● Keywords:
● Alias: groups_by_filter
● 0 images

ihw.DESeqResults (Package: IHW) : ihw.DESeqResults: IHW method dispatching on DESeqResults objects

ihw.DESeqResults: IHW method dispatching on DESeqResults objects

● Data Source: BioConductor
● Keywords:
● Alias: ihw.DESeqResults
● 0 images

ihw.default (Package: IHW) : ihw: Main function for Independent Hypothesis Weighting

Given a vector of p-values, a vector of covariates which are independent of the p-values under the null hypothesis and a nominal significance level alpha, IHW learns multiple testing weights and then applies the weighted Benjamini Hochberg (or Bonferroni) procedure.

● Data Source: BioConductor
● Keywords:
● Alias: ihw, ihw.default, ihw.formula
● 0 images

ihwResult-class (Package: IHW) : An S4 class to represent the ihw output.

An S4 class to represent the ihw output.

● Data Source: BioConductor
● Keywords:
● Alias: adj_pvalues, adj_pvalues,ihwResult-method, alpha, alpha,ihwResult-method, as.data.frame,ihwResult-method, as.data.frame_ihwResult, covariate_type, covariate_type,ihwResult-method, covariates, covariates,ihwResult-method, groups_factor, groups_factor,ihwResult-method, ihwResult, ihwResult-class, m_groups, m_groups,ihwResult-method, nbins, nbins,ihwResult-method, nfolds, nfolds,ihwResult-method, nrow,ihwResult-method, pvalues, pvalues,ihwResult-method, regularization_term, regularization_term,ihwResult-method, rejected_hypotheses, rejected_hypotheses,ihwResult-method, rejections, rejections,ihwResult-method, show,ihwResult-method, thresholds, thresholds,ihwResult-method, weighted_pvalues, weighted_pvalues,ihwResult-method, weights,ihwResult-method
● 0 images

plot,ihwResult-method (Package: IHW) : Convenience function to plot weights learned by ihw method

Convenience function to plot weights learned by ihw method

● Data Source: BioConductor
● Keywords:
● Alias: plot,ihwResult-method
● 1 images