Package: metapod 1.21.0

Aaron Lun

metapod: Meta-Analyses on P-Values of Differential Analyses

Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for corresponding tests across separate analyses (e.g., replicated comparisons, effect of different treatment conditions). Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate.

Authors:Aaron Lun [aut, cre]

metapod_1.21.0.tar.gz
metapod_1.21.0.zip(r-4.7)metapod_1.21.0.zip(r-4.6)metapod_1.21.0.zip(r-4.5)
metapod_1.21.0.tgz(r-4.6-x86_64)metapod_1.21.0.tgz(r-4.6-arm64)metapod_1.21.0.tgz(r-4.5-x86_64)metapod_1.21.0.tgz(r-4.5-arm64)
metapod_1.21.0.tar.gz(r-4.7-arm64)metapod_1.21.0.tar.gz(r-4.7-x86_64)metapod_1.21.0.tar.gz(r-4.6-arm64)metapod_1.21.0.tar.gz(r-4.6-x86_64)
metapod_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
metapod/json (API)

# Install 'metapod' in R:

install.packages('metapod', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ltla/metapod/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:metapod-1.21.0(bioc 3.24)metapod-1.20.0(bioc 3.23)

multiplecomparison differentialpeakcalling cpp

7.41 score 2 stars 54 packages 20 scripts 22 exports 1 dependencies

Last updated from:b1a66ff483. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	161
linux-devel-arm64	NOTE	184
linux-devel-x86_64	NOTE	188
source / vignettes	OK	210
linux-release-arm64	NOTE	146
linux-release-x86_64	NOTE	196
macos-release-arm64	NOTE	135
macos-release-x86_64	NOTE	291
macos-oldrel-arm64	NOTE	147
macos-oldrel-x86_64	NOTE	296
windows-devel	NOTE	166
windows-release	NOTE	142
windows-oldrel	NOTE	143
wasm-release	OK	122

Exports:averageGroupedStats averageParallelStats combineGroupedPValues combineParallelPValues countGroupedDirection countParallelDirection groupedBerger groupedFisher groupedHolmMin groupedPearson groupedSimes groupedStouffer groupedWilkinson parallelBerger parallelFisher parallelHolmMin parallelPearson parallelSimes parallelStouffer parallelWilkinson summarizeGroupedDirection summarizeParallelDirection

Dependencies:Rcpp

Meta-analyses on p-values of various differential tests

Rendered fromoverview.Rmdusingknitr::rmarkdown

Last update: 2021-05-12
Started: 2020-11-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
metapod: Meta-Analyses on P-Values of Differential Analyses	metapod-package metapod
Average grouped statistics	averageGroupedStats
Average parallel statistics	averageParallelStats
Combine grouped p-values	combineGroupedPValues
Combine parallel p-values	combineParallelPValues
Count directions of grouped tests	countGroupedDirection
Count directions of parallel tests	countParallelDirection
Combine grouped p-values with Berger's IUT	groupedBerger
Combine grouped p-values with Fisher's method	groupedFisher
Combine grouped p-values with the minimum Holm approach	groupedHolmMin
Combine grouped p-values with Pearson's method	groupedPearson
Combine grouped p-values with Simes' method	groupedSimes
Combine grouped p-values with Stouffer's Z-score method	groupedStouffer
Combine grouped p-values with Wilkinson's method	groupedWilkinson
Combine parallel p-values with Berger's IUT	parallelBerger
Combine parallel p-values with Fisher's method	parallelFisher
Combine parallel p-values with the minimum Holm approach	parallelHolmMin
Combine parallel p-values with Pearson's method	parallelPearson
Combine parallel p-values with Simes' method	parallelSimes
Combine parallel p-values with Stouffer's Z-score	parallelStouffer
Combine p-values with Wilkinson's method	parallelWilkinson
Summarize overall direction of grouped tests	summarizeGroupedDirection
Summarize overall direction of parallel tests	summarizeParallelDirection