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- Title
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.
- Authors
Pedersen, Brent S; Schwartz, David A; Yang, Ivana V; Kechris, Katerina J
- Abstract
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.
- Publication
Bioinformatics (Oxford, England), 2012, Vol 28, Issue 22, p2986
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/bts545