MPAC
Bioc currentMulti-omic Pathway Analysis of Cells
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
Multi-omic Pathway Analysis of Cells (MPAC), integrates multi-omic data for understanding cellular mechanisms. It predicts novel patient groups with distinct pathway profiles as well as identifying key pathway proteins with potential clinical associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA states (i.e., repressed, normal, or activated), which serve as the input for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes DNA and RNA states to create a background distribution to filter IPLs as a way to remove events observed by chance. It provides multiple methods for downstream analysis and visualization.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
45 20 exported
Complexity
1.6 avg / 6 max
Call network
45 nodes / 31 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
3,328
Files
115
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
20
Internal functions
25
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.29
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
90.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2024-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 20
- Examples that run
- 100%19 run in a plain check
- Exported functions with examples
- 95%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/pliu55/mpac on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| TCGA-CV-7100_1_cfg | data.frame | 5 × 2 | No other package |
| TCGA-CV-7100_1_cpt | data.frame | 20 × 3 | No other package |
| TCGA-CV-7100_1_inp_focal | data.frame | 1 × 8 | No other package |
| TCGA-CV-7100_1_inp_log10fpkmP1 | data.frame | 1 × 8 | No other package |
| TCGA-CV-7100_1_ipl | – | – | – |
| TCGA-CV-7100_2_cfg | data.frame | 5 × 2 | No other package |
| TCGA-CV-7100_2_cpt | data.frame | 20 × 3 | No other package |
| TCGA-CV-7100_2_inp_focal | data.frame | 1 × 8 | No other package |
| TCGA-CV-7100_2_inp_log10fpkmP1 | data.frame | 1 × 8 | No other package |
| TCGA-CV-7100_2_ipl | – | – | – |
| TCGA-CV-7100_3_cfg | data.frame | 5 × 2 | No other package |
| TCGA-CV-7100_3_cpt | data.frame | 20 × 3 | No other package |
| TCGA-CV-7100_3_inp_focal | data.frame | 1 × 8 | No other package |
| TCGA-CV-7100_3_inp_log10fpkmP1 | data.frame | 1 × 8 | No other package |
| TCGA-CV-7100_3_ipl | – | – | – |
| TCGA-CV-7100_cfg | data.frame | 5 × 2 | No other package |
| TCGA-CV-7100_cpt | data.frame | 20 × 3 | No other package |
| TCGA-CV-7100_inp_focal | data.frame | 1 × 8 | No other package |
| TCGA-CV-7100_inp_log10fpkmP1 | data.frame | 1 × 8 | No other package |
| TCGA-CV-7100_ipl | – | – | – |
| cdr | matrix | 71 × 4 | No other package |
| cl | data.table | 15 × 72 | No other package |
| clmat | matrix | 18 × 1 | No other package |
| con_grph | list | 1 element | No other package |
| flt_real | matrix | 30 × 2 | No other package |
| fltmat | matrix | 7 × 11 | No other package |
| focal_tumor | matrix | 7 × 71 | No other package |
| grphl | list | 4 elements | No other package |
| inp_focal | – | – | – |
| inp_log10fpkmP1 | – | – | – |
| inp_perm | list | 3 elements | 2 packages |
| inp_real | – | – | – |
| ipl | matrix | 8 × 71 | No other package |
| log10fpkmP1_normal | matrix | 7 × 44 | No other package |
| log10fpkmP1_tumor | matrix | 7 × 71 | No other package |
| ovr | matrix | 2 × 2 | No other package |
| ovrmat | matrix | 2,085 × 18 | No other package |
| perm | data.table | 90 × 3 | No other package |
| real | data.table | 30 × 2 | No other package |
| subntwl | list | 2 elements | No other package |
| tiny_pth | – | – | – |
Topics
People
- Peng Liu author maintainer
- Paul Ahlquist author
- Anthony Gitter author
- Irene Ong author
Cite
Cite this package
Run in R for the authors' entry:
citation("MPAC")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btaf490.
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.