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Bioinformatics. 2012 Nov 15;28(22):2986-8. doi: 10.1093/bioinformatics/bts545. Epub 2012 Sep 5.

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

Author information

  • 1Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA. bpederse@gmail.com

Abstract

SUMMARY:

comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions. In addition, tools are provided for visualization and assessment. We provide validation and example uses on bisulfite-seq with P-values from Fisher's exact test, tiled methylation probes using a linear model and Dam-ID for chromatin binding using moderated t-statistics. Because the library accepts input in a simple, standardized format and is unaffected by the origin of the P-values, it can be used for a wide variety of applications.

AVAILABILITY:

comb-p is maintained under the BSD license. The documentation and implementation are available at https://github.com/brentp/combined-pvalues.

CONTACT:

bpederse@gmail.com

PMID:
22954632
[PubMed - indexed for MEDLINE]
PMCID:
PMC3496335
Free PMC Article
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