Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA.
Bioinformatics. 2012 Nov 15;28(22):2986-8. doi: 10.1093/bioinformatics/bts545. Epub 2012 Sep 5.
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.
comb-p is maintained under the BSD license. The documentation and implementation are available at https://github.com/brentp/combined-pvalues.
comb-p 是一个命令行工具和一个 Python 库，用于操作可能具有不规则间隔 P 值的 BED 文件，并执行以下操作：（1）计算自相关；（2）合并相邻 P 值；（3）进行错误发现调整；（4）找到富集区域（即一系列相邻的低 P 值）；（5）为这些区域分配显著性。此外，还提供了可视化和评估工具。我们提供了在使用 Fisher 精确检验的亚硫酸盐测序、使用线性模型的平铺甲基化探针以及使用修正 t 统计量的染色质结合的 Dam-ID 的 P 值方面的验证和示例使用。由于该库接受简单、标准化的格式输入，并且不受 P 值来源的影响，因此它可以用于各种应用。
comb-p 遵循 BSD 许可证进行维护。文档和实现可在 https://github.com/brentp/combined-pvalues 上获得。
