In:
Bioinformatics, Oxford University Press (OUP), Vol. 28, No. 22 ( 2012-11-15), p. 2986-2988
Kurzfassung:
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
Materialart:
Online-Ressource
ISSN:
1367-4811
,
1367-4803
DOI:
10.1093/bioinformatics/bts545
Sprache:
Englisch
Verlag:
Oxford University Press (OUP)
Publikationsdatum:
2012
ZDB Id:
1468345-3
SSG:
12
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