R/rarefy.func.R

In hk1785/MiVT: Microbiome Virtual Twins

rarefy.func <-
function(biom, cut.off, multi.rarefy = FALSE) {
  
  if (!multi.rarefy | multi.rarefy == 1) {
    biom <- rarefy_even_depth(biom, cut.off, rngseed = 123)
  } else {
    otu.tab <- otu_table(biom)
    tax.tab <- tax_table(biom)
    tree <- phy_tree(biom)
    sam.dat <- sample_data(biom)
    
    otu.tab.list <- list()
    for (i in 1:multi.rarefy) {
      otu.tab.list[[i]] <- otu_table(rarefy_even_depth(biom, cut.off, rngseed = i), taxa_are_rows = TRUE)
    }
    
    sum.otu.tab <- otu.tab.list[[1]]
    for (i in 2:multi.rarefy) {
      sum.otu.tab <- sum.otu.tab + otu.tab.list[[i]]
    }
    otu.tab <- otu_table(round(sum.otu.tab/multi.rarefy), taxa_are_rows = TRUE)
    biom <- merge_phyloseq(otu.tab, tax.tab, tree, sam.dat) 
  }
  
  return(biom)
}