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使用 GenometriCorr 包探索大规模基因组数据集。

Exploring massive, genome scale datasets with the GenometriCorr package.

机构信息

Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.

出版信息

PLoS Comput Biol. 2012 May;8(5):e1002529. doi: 10.1371/journal.pcbi.1002529. Epub 2012 May 31.

DOI:10.1371/journal.pcbi.1002529
PMID:22693437
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3364938/
Abstract

UNLABELLED

We have created a statistically grounded tool for determining the correlation of genomewide data with other datasets or known biological features, intended to guide biological exploration of high-dimensional datasets, rather than providing immediate answers. The software enables several biologically motivated approaches to these data and here we describe the rationale and implementation for each approach. Our models and statistics are implemented in an R package that efficiently calculates the spatial correlation between two sets of genomic intervals (data and/or annotated features), for use as a metric of functional interaction. The software handles any type of pointwise or interval data and instead of running analyses with predefined metrics, it computes the significance and direction of several types of spatial association; this is intended to suggest potentially relevant relationships between the datasets.

AVAILABILITY AND IMPLEMENTATION

The package, GenometriCorr, can be freely downloaded at http://genometricorr.sourceforge.net/. Installation guidelines and examples are available from the sourceforge repository. The package is pending submission to Bioconductor.

摘要

未加标签

我们创建了一个基于统计学的工具，用于确定全基因组数据与其他数据集或已知生物学特征的相关性，旨在指导对高维数据集的生物学探索，而不是提供直接答案。该软件支持对这些数据进行几种基于生物学的方法，这里我们描述了每种方法的原理和实现。我们的模型和统计数据在一个 R 包中实现，该包可以有效地计算两组基因组区间（数据和/或注释特征）之间的空间相关性，用作功能相互作用的度量。该软件可以处理任何类型的点状或区间数据，而不是使用预定义的指标运行分析，它计算几种类型的空间关联的显著性和方向；这旨在提示数据集之间可能存在的相关关系。

可用性和实现

软件包 GenometriCorr 可以在 http://genometricorr.sourceforge.net/ 上免费下载。安装指南和示例可从 sourceforge 存储库获得。该软件包正在提交给 Bioconductor。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/8f0f05c10309/pcbi.1002529.g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/cec1180ff8d9/pcbi.1002529.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/5034ecdbb6c1/pcbi.1002529.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/96b4b168c64e/pcbi.1002529.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/bfa9469e9b26/pcbi.1002529.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/223441d77600/pcbi.1002529.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/fb1f6473f5f5/pcbi.1002529.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/7b19d2d34cd1/pcbi.1002529.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/8fd87e3024b7/pcbi.1002529.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/8f0f05c10309/pcbi.1002529.g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/cec1180ff8d9/pcbi.1002529.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/5034ecdbb6c1/pcbi.1002529.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/96b4b168c64e/pcbi.1002529.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/bfa9469e9b26/pcbi.1002529.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/223441d77600/pcbi.1002529.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/fb1f6473f5f5/pcbi.1002529.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/7b19d2d34cd1/pcbi.1002529.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/8fd87e3024b7/pcbi.1002529.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9fc0/3364938/8f0f05c10309/pcbi.1002529.g009.jpg

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