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Pirat

Bioc current

Precursor or Peptide Imputation under Random Truncation

v1.6.0 · software · GPL-2
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.20 · Oct 30, 2024

Current · Requires R 4.6

1.0 In 4 of 49 releases 3.23

Description

Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

15 15 exported

Complexity

5.6 avg / 23 max

Call network

15 nodes / 11 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

2,470

Files

50

Compiled share

0%

Has compiled src

No

Language breakdown

R 1,404 (56.8%)Docs 758 (30.7%)Vignettes 308 (12.5%)

API

Exported functions

16

Internal functions

0

Recent export changes

v3.20+16 envPirat, estimate_gamma, estimate_psi_df +13 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

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

4.5.0

System requirements

–

C++ standard

–

License

GPL-2

License flags

SPDX valid, OSI approved

History

Versions

4

First release

2025-03-03

Latest release

2026-04-28

Avg cadence

168 days

Cold removal rate

–

Dep drift

1

LOC over versions

v3.20: 2,450 LOCv3.21: 2,454 LOCv3.22: 2,470 LOCv3.23: 2,470 LOC

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

Documentation

Documentation
READMEYes · 57 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo
Examples that run
79%
Documented parameters
100%
Return-value docs
100%
References docs
17%

Topics

Software › ResearchField › Proteomics
Software › Technology › MassSpectrometry
Software › WorkflowStep › Preprocessing
Software

Depended on by (1)

Bioconductor (1)

DaparToolshed

People

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