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

被引：311

作者：

Pedersen, Brent S. ^{[1
]}

Schwartz, David A. ^{[1
]}

Yang, Ivana V. ^{[1
]}

Kechris, Katerina J. ^{[2
]}

机构：

[1] Univ Colorado, Dept Med, Aurora, CO 80045 USA

[2] Univ Colorado, Dept Biostat & Informat, Aurora, CO 80045 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 22期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/bioinformatics/bts545

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2986 / 2988

页数：3

共 13 条

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