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ramwas

Bioc current

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

v1.36.0 · software · LGPL-3
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.5 · Apr 25, 2017

Current · Requires R 4.6

1.0 In 19 of 49 releases 3.23

Description

A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) <doi:10.1093/bioinformatics/bty069>.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

132 55 exported

Complexity

4 avg / 67 max

Call network

132 nodes / 180 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

11,093

Files

75

Compiled share

1.1%

Has compiled src

Yes

Language breakdown

R 5,600 (50.5%)C/C++/src 118 (1.1%)Docs 2,436 (22%)Vignettes 2,939 (26.5%)

API

Exported functions

55

Internal functions

71

Recent export changes

v3.7+19 qqPlotPrepare, manPlotPrepare, manPlotFast +16 more  −1 getTestsByLocation
v3.5+37 ramwasParameters, ramwasAnnotateLocations, isAbsolutePath +34 more

Testing & CI

Has tests

No

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.3.0

System requirements

–

C++ standard

–

License

LGPL-3

License flags

SPDX valid, OSI approved

History

Versions

19

First release

2017-04-24

Latest release

2026-04-28

Avg cadence

183 days

Cold removal rate

100%

Dep drift

0

LOC over versions

v3.5: 8,638 LOCv3.6: 8,638 LOCv3.7: 10,645 LOCv3.8: 10,646 LOCv3.9: 11,093 LOCv3.10: 11,093 LOCv3.11: 11,093 LOCv3.12: 11,093 LOCv3.13: 11,093 LOCv3.14: 11,093 LOCv3.15: 11,093 LOCv3.16: 11,093 LOCv3.17: 11,093 LOCv3.18: 11,093 LOCv3.19: 11,093 LOCv3.20: 11,093 LOCv3.21: 11,093 LOCv3.22: 11,093 LOCv3.23: 11,093 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

Documentation
READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo
Examples that run
93%
Documented parameters
98%
Return-value docs
100%
References docs
0%

Topics

Software › AssayDomain › DNAMethylation
Software › Technology › Sequencing
Software › WorkflowStep › QualityControl
Software › BiologicalQuestion › Coverage
Software › WorkflowStep › Preprocessing
Software › WorkflowStep › Normalization
Software › WorkflowStep › BatchEffect
Software › StatisticalMethod › PrincipalComponent
Software › BiologicalQuestion › DifferentialMethylation
Software › WorkflowStep › Visualization

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