Clean Taxonomy

Source: R/cleanTaxonomy.R

Clean Taxonomy

cleanTaxonomy(x)

Arguments

x

A phyloseq object

Value

phyloseq

Details

Removes, special characters, spaces and prefixes in tax_table.

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("FuentesIliGutData")
ps1 <- cleanTaxonomy(FuentesIliGutData)
ps1
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 905 taxa and 589 samples ]
#> sample_data() Sample Data:       [ 589 samples by 61 sample variables ]
#> tax_table()   Taxonomy Table:    [ 905 taxa by 7 taxonomic ranks ]
#> phy_tree()    Phylogenetic Tree: [ 905 tips and 904 internal nodes ]