## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library(mbOmic) library(data.table) ## ----------------------------------------------------------------------------- dat <- read.delim('http://enterotypes.org/ref_samples_abundance_MetaHIT.txt') dat <- impute::impute.knn(as.matrix(dat), k = 100) dat <- as.data.frame(dat$data+0.001) setDT(dat, keep.rownames = TRUE) dat ## ----------------------------------------------------------------------------- dat <- bSet(b = dat) res <- estimate_k(dat) res ## ----------------------------------------------------------------------------- ret=enterotyping(dat, res$verOptCluster) ret ## ----------------------------------------------------------------------------- enterotypes <- read.table(system.file('extdata', 'enterotype.txt', package = 'mbOmic')) enterotypes <- enterotypes[samples(dat),] table(res$verOptCluster, enterotypes$ET) ## ----------------------------------------------------------------------------- devtools::session_info()