PyRRA 0.1.0

Port of RobustRankAggreg for robust aggregate ranking in Python.

PyRRA: Python Implementation of the RobustRankAggreg R package

Disclaimer: The PyRRA (Python Robust Rank Aggregation) project is an attempted port of the RobustRankAggreg R package (v1.2.1; cran.r-project.org/web/packages/RobustRankAggreg). PyRRA is under development and the outputs between the original R package and this Python implementation are not guaranteed to be identical. This python reimplementation is independent of the original authors and code maintainers (DOI: 10.1093/bioinformatics/btr709).

A Python port of the RobustRankAggreg (RRA) package for robust aggregation of ranked lists with missing/unmatched elements. PyRRA enables reproducible meta-analyses, gene integration, and other robust ranking applications right from Python.

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Features

• PyRRA is still under development
• Robust aggregation of partial or full ranked lists (no requirement that sets overlap)
• Ports of RRA's rankMatrix, betaScores, rhoScores, and all aggregation methods (RRA, stuart, mean, min, median, geom.mean)
• Validated with cross-language testing against the original R package
• Helper utilities for thresholding, multiple testing correction, and Stuart p-value computation

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Installation

Suggested Conda environment:

conda env create -f environment.yml 
conda activate pyrra

Install from PyPi (recommended):

pip install pyrra

Install directly from source via pip:

pip install .

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Usage

from pyrra import rank_matrix, aggregate_ranks

# A list of ranked gene symbols (or any unique items)
glists = [
    ['b', 'c', 'd', 'a'],
    ['h', 'b', 'f', 'e', 'd', 'c', 'g', 'a', 'j', 'i'],
    ['m', 'l', 'k', 'j', 'i', 'h', 'g', 'f', 'e', 'd', 'c', 'b']
]

rank_mat = rank_matrix(glists)
print(rank_mat)
#           L1   L2   L3
# a  1.000000 0.125  NaN
# b  0.250000 0.175 0.917
# ...

# Aggregate with the default RRA method
agg = aggregate_ranks(glist=glists, method='RRA')
print(agg.head())
#     Name     Score
# 0      ...     ...

You can also pass a pandas DataFrame rank matrix to aggregate_ranks via rmat=....

Aggregation Methods

• RRA (default)
• stuart: Stuart-Aerts p-value
• min, mean, median, geom.mean: Aggregate using these statistics

Advanced Arguments

• full (default=False): Set True if all input lists are full rankings (for structural NA treatment)
• N: Total number of rankable items (overrides default: union of elements)
• exact (default: auto): Use exact p-value (slower, may be numerically unstable for many lists)
• top_cutoff: Vector of cutoff values (for sensitivity when lists are truncated at different points)

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API Reference

rank_matrix(glist, N=None, full=False)

• Converts ranked lists to a normalized rank matrix.
• Parameters:
  • glist: list of lists
  • N: total number of rankable elements (default: union of glist)
  • full: If True, treat all as full-length rankings with NA for structural gaps
• Returns: pandas DataFrame

aggregate_ranks(glist=None, rmat=None, N=None, method='RRA', full=False, exact=None, top_cutoff=None)

• Main aggregation method (RRA, mean, min, etc).
• Returns: pandas DataFrame of scores, sorted.

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Citing

• Original algorithm: RobustRankAggreg Bioinformatics 2012

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Contributors

Elly Poretsky (@eporetsky) — Python port, test suite, data validation.

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See Also

• RobustRankAggreg (R Package)

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Comparison with the R implementation

For users seeking direct comparison and validation against the original R RobustRankAggreg package, see the output in compare/comprehensive_comparison.txt or follow the instructions below to run your own validations:

cd compare

# Conda environment with Python and R
conda env create -f environment.yml 
conda activate pyrra_compare
pip install pyrra

# Run tests to comparee
python comprehensive_comparison.py