R/otu.tab.clean.R

In hk1785/MiVT: Microbiome Virtual Twins

otu.tab.clean <-
function(biom, lib.size.cut.off = 1000, mean.prop.cut.off = mean.prop.cut.off) {
  
  otu.tab <- otu_table(biom)
  tax.tab <- tax_table(biom)
  tree <- phy_tree(biom)
  sam.dat <- sample_data(biom)
  
  lib.size <- colSums(otu.tab)
  ind.low.lib.size <- which(lib.size > lib.size.cut.off)
  lib.size <- lib.size[ind.low.lib.size]
  otu.tab <- otu.tab[,ind.low.lib.size]
  sam.dat <- sam.dat[ind.low.lib.size,]
  
  prop.otu.tab <- otu.tab
  for (i in 1:length(lib.size)) {
    prop.otu.tab[,i] <- otu.tab[,i]/lib.size[i]
  }
  mean.prop <- rowMeans(prop.otu.tab)
  ind.low.mean.prop <- which(mean.prop >= mean.prop.cut.off)
  taxa <- rownames(otu.tab)[ind.low.mean.prop]
  biom <- merge_phyloseq(otu.tab, tax.tab, tree, sam.dat)
  biom <- prune_taxa(taxa, biom)
  
  return(biom)  
}