Package: IHW 1.35.0

Nikos Ignatiadis

IHW: Independent Hypothesis Weighting

Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.

Authors:Nikos Ignatiadis [aut, cre], Wolfgang Huber [aut]

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IHW.pdf |IHW.html✨
IHW/json (API)

# Install 'IHW' in R:
install.packages('IHW', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:IHW-1.35.0(bioc 3.21)IHW-1.34.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologymultiplecomparisonrnaseq

7.22 score 2 packages 248 scripts 1.4k downloads 8 mentions 22 exports 5 dependencies

Last updated 2 months agofrom:a1c2d79c7d. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 13 2024
R-4.5-winNOTEDec 13 2024
R-4.5-linuxNOTEDec 13 2024
R-4.4-winNOTEDec 13 2024
R-4.4-macNOTEDec 13 2024
R-4.3-winNOTEDec 13 2024
R-4.3-macNOTEDec 13 2024

Exports:adj_pvaluesalphaas.data.framecovariate_typecovariatesget_bh_thresholdgroups_by_filtergroups_factorihwm_groupsnbinsnfoldsnrowplotpvaluesregularization_termrejected_hypothesesrejectionsshowthresholdsweighted_pvaluesweights

Dependencies:BiocGenericsfdrtoolgenericslpsymphonyslam

Introduction to Independent Hypothesis Weighting with the IHW Package

Nikos Ignatiadis, Wolfgang Huber

Rendered fromintroduction_to_ihw.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2016-10-03
Started: 2016-01-31

Readme and manuals

Help Manual

Help pageTopics
Data-driven threshold of Benjamini Hochberg Procedureget_bh_threshold
Stratify hypotheses based on increasing value of the covariategroups_by_filter
ihw: Main function for Independent Hypothesis Weightingihw ihw.default ihw.formula
ihw.DESeqResults: IHW method dispatching on DESeqResults objectsihw.DESeqResults
An S4 class to represent the ihw output.adj_pvalues adj_pvalues,ihwResult-method alpha alpha,ihwResult-method as.data.frame,ihwResult-method as.data.frame_ihwResult covariates covariates,ihwResult-method covariate_type covariate_type,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
Plot functions for IHWplot,ihwResult-method