IHWpaper
Bioc currentReproduce figures in IHW paper
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
49 29 exported
Complexity
1.7 avg / 8 max
Call network
49 nodes / 14 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
4,452
Files
140
Compiled share
1.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
29
Internal functions
17
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.3
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-05-15
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 19
- Examples that run
- 100%18 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 95%
- Return-value docs
- 100%
- Help pages citing references
- 21%
- Various: BH explanation / visualization HTML
- NMeth paper: Explaining tdr HTML
- Various: Grenander Estimator as applied to IHW (vs ECDF) HTML
- Stats paper: hQTL analysis with IHW-Benjamini-Yekutieli HTML
- NMeth paper: IHW-Bonferroni simulations HTML
- Various: Real data examples: 1-fold weight function HTML
- NMeth paper: Real data examples HTML
- NMeth paper: Simulation Figures HTML
- NMeth paper: Stratified Histograms HTML
- Various: tdr and pvalue rejection regions HTML
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Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
1 practice detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| bottomly.eset | – | – | – |
| hammer.eset | – | – | – |
| hqtl_estimated_lfdrs | data.frame | 124 × 9 | No other package |
| hqtl_pvalue_filtered | data.frame | 976,472 × 3 | No other package |
| m_groups_chr1 | table | 62 | No other package |
| m_groups_chr2 | table | 62 | No other package |
| peak_locations | tibble | 135,873 × 4 | No other package |
| science_signaling | – | – | – |
| snppos_chr1 | tibble | 645,452 × 6 | No other package |
| snppos_chr2 | tibble | 699,343 × 6 | No other package |
Topics
People
- Nikos Ignatiadis author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("IHWpaper")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/nmeth.3885.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.