In gongcongcong/mbOmic: Integrative analysis of the microbiome and metabolome

knitr::opts_chunk$set(
  collapse = TRUE,
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A workflow for identifying enterotypes based on the relative abundance of gut microbiota was implemented refereed on the reports of Arumugam[^2]

[^1]: Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., ... & Bork, P. (2011). Enterotypes of the human gut microbiome. nature, 473(7346), 174-180.

library(mbOmic)
library(data.table)

First of all, the dataset of microbiota relative abundance was retrived from the enterotypes weblink. The missing value was imputed using KNN by impute package.

# dat <- read.delim('http://enterotypes.org/ref_samples_abundance_MetaHIT.txt')
# dat <- impute::impute.knn(as.matrix(dat), k = 100)
# dat <- as.data.frame(dat$data+0.001) 
# setDT(dat, keep.rownames = TRUE)
# dat

Constructe the bSet class and then estimate the the proper cluster number using the estimate_k function. The estimate_k function take advantage of Jensen-Shannon divergence to cluster the samples and the number of clusters was optimizated by Calinski-Harabasz (CH) Index and Silhouette Coefficient.

The estimate_k returns verCHI class, a S3 class containing a optimal cluster results, optimal number cluster, a minmum CHI, a minmum Silhouette value, and Jensen-Shannon divergence matrix.

# dat <- bSet(b =  dat)
# res <- estimate_k(dat)
# res

The proper number of cluster is 4.

Next, the enterotyping function was used to identify the enterotype for each cluster and it returns a 3-length list. This list contains two enterotypes matrices and a unidentified samples vector. Cluster 2, 3, and 4 was enterotype Bacteroides, Prevotella, and Ruminococcus, resepectively.

# ret=enterotyping(dat, res$verOptCluster) 
# ret

Furthermore, this result was validated by enterotypes results given by the enterotype website.

# enterotypes <- read.table(system.file('extdata', 'enterotype.txt', package = 'mbOmic'))
# enterotypes <- enterotypes[samples(dat),]
# table(res$verOptCluster, enterotypes$ET)