Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• The comb-p tool is available under the BSD license.
• Documentation and source code are accessible via GitHub.

Purpose of the Study:

• To introduce comb-p, a flexible command-line tool and Python library.
• To provide functionalities for P-value manipulation and analysis in genomic data.

Main Methods:

• Utilizes BED files for handling P-values of varying spacing.
• Implements functions for auto-correlation, P-value combination, and false discovery rate adjustment.
• Includes methods for identifying and assessing regions of P-value enrichment.

Main Results:

• Demonstrates validation and application on bisulfite-seq, tiled methylation probes, and Dam-ID data.
• Shows utility with P-values derived from Fisher's exact test, linear models, and moderated t-statistics.
• Highlights the tool's adaptability due to its standardized input format and P-value origin independence.

Conclusions:

• comb-p offers a comprehensive solution for P-value analysis across diverse genomic applications.
• The tool's flexibility makes it suitable for a wide range of biological research questions.
• Provides integrated visualization and assessment tools for enhanced data interpretation.