计算微生物otu表格组间差异

ANOSIM相似性分析是一种非参数检验，用来检验组间（两组或多组）差异是否显著大于组内差异，从而判断分组是否有意义。首先利用Bray-Curtis算法计算两两样品间的距离，然后将所有距离从小到大进行排序，并计算R和P值。

library(vegan)

type = read.table("sample-metadata2.txt", header=T, row.names=1, sep="\t", comment.char="")

beta_bray_curtis = read.table("bacteria3.txt", header=T, row.names=1, sep="\t", comment.char="")

anosim(beta_bray_curtis,type$Type,permutations = 999,distance = 'bray')

#Call:

#  anosim(x = beta_bray_curtis, grouping = type$Type, permutations = 999,      distance = "bray")

#Dissimilarity: bray

#ANOSIM statistic R: 0.7143

#Significance: 0.001

#Permutation: free

#Number of permutations: 999