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在R中规范化系统树

[英]Normalizing a Phylogenetic Tree in R

原文 2011-07-27 03:50:06 7 1 r/ statistics/ normalization/ phylogeny/ ape-phylo

When working with phylogenetic tree data in R (specifically when working with "phylo" or "phylo4" objects) it would be useful to normalize branch lengths so that certain taxa (the ones that evolve faster) do not contribute a disproportionate amount of branch length to the tree. 当使用R中的系统发生树数据时（特别是当使用“ phylo”或“ phylo4”对象时），标准化分支长度将很有用，这样某些分类单元（进化较快的分类单元）不会对分支长度产生不成比例的影响到树上。 This seems to be common in computing UniFrac values, as can be found in the discussion here: http://bmf2.colorado.edu/unifrac/help.psp . 这在计算UniFrac值中似乎很常见，可以在以下讨论中找到： http ://bmf2.colorado.edu/unifrac/help.psp。 (I need more than just UniFrac values, however). （不过，我不仅需要UniFrac值）。

However, I cannot find a function that performs this normalization step. 但是，我找不到执行此标准化步骤的函数。 I have looked in ape, picante, adephylo, and phylobase. 我看过猿，picante，adephylo和phylobase。 Could someone direct me to a package that includes this function, or a package that makes writing this kind of function straightforward? 有人可以将我定向到包含此功能的程序包，还是使编写此类功能的程序简单明了的程序包？

1 个解决方案

Are you looking for a function to just scale the branch lengths of a tree? 您是否正在寻找一种功能来缩放树的分支长度？ If so, compute.brlen() in ape will do it. 如果是这样，猿中的compute.brlen()会做到这一点。 There are built in options for Grafen's rho and all = 1. You can also supply your own function. Grafen的rho有内置选项，all =1。您也可以提供自己的功能。

I don't know if UniFrac does some other kind of branch length scaling. 我不知道UniFrac是否进行其他种类的分支长度缩放。 But if so, you could write your function and pass it. 但是，如果是这样，您可以编写函数并通过它。