Mothur-metastats command(metastat丰度差异分析)

基于各分类学水平样品序列数的统计信息,可以比较某一特定物种在两个(组)样品之间丰度的差异情况,在统计学上是否存在显著性差异。

输入:

OTU Table文件:

OTU ID   Bio1 Bio2 Bio3 Bio4  Bio5  Bio6 Bio7 Bio8 Bio9 Bio10

OTU1       0      0       0       0       0       6     34   104   367   254

OTU2      52   335    18     49      0       0      0      0       0       0

OTU3       0      0       0       0       5       0      0      0       0       0

样品分组信息表:

!!注:保证每个分组包含的样品数量不少于2>=2),即每个分组都需要有重复样。

Bio1 group1

Bio2 group1

Bio3 group1

Bio4 group1

Bio5 group2

Bio6 group2

Bio7 group2

Bio8 group2

其他参数默认。

输出:

组间丰度差异分析结果:

OTU mean(group1)  variance(group1)      stderr(group1)   mean(group2)  variance(group2)      stderr(group2)   p-value     q-value

OTU1        0.001123 0.000002 0.000666 0.000000 0.000000 0.000000 0.044141 0.096941

OTU2        0.000000 0.000000 0.000000 0.003412 0.000022 0.002356 0.099423 0.120657

OTU3        0.000042 0.000000 0.000042 0.000000 0.000000 0.000000 0.314421 0.137950

OTU4        0.000000 0.000000 0.000000 0.000291 0.000000 0.000102 0.001928 0.027043

OTU5        0.000000 0.000000 0.000000 0.000013 0.000000 0.000013 0.503021 0.214902

OTU6        0.000033 0.000000 0.000024 0.000146 0.000000 0.000091 0.180469 0.137950

OTU7        0.004893 0.000007 0.001321 0.000000 0.000000 0.000000 0.000412 0.018450

分析模块引用了mothurv.1.35.0)的metastats命令。

相关文献如下所示:

Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

The original tools:

Schloss, PD & Handelsman, J. (2006) Introducing SONS, a tool for OTU-based comparisons of membership and structure between microbial communities. Applied and Environmental Microbiology. 72:6773-9.

Schloss, PD & Handelsman, J. (2006). Introducing TreeClimber, a test to compare community structures. Applied and Environmental Microbiology. 72: 2379-84.

Schloss, PD & Handelsman, J. (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology. 71:1501-6.

Schloss, PD, Larget, BR, & Handelsman J. (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Applied and Environmental Microbiology. 70:5485-92.