Rename the samples of a phyloseq slot

Useful for targets bioinformatic pipeline.

Usage

rename_samples(phyloseq_component, names_of_samples, taxa_are_rows = FALSE)

Arguments

phyloseq_component

(required) one of otu_table or sam_data slot of a phyloseq-class object

names_of_samples

(required) A vector of samples names

taxa_are_rows

(default to FALSE) see ?phyloseq for details

Value

The otu_table or the sam_data slot with new samples names

Author

Adrien Taudière

Examples

otutab <- rename_samples(
  data_fungi@otu_table,
  paste0("data_f", sample_names(data_fungi))
)
otutab2 <- rename_samples(
  clean_pq(data_fungi,
    force_taxa_as_rows = TRUE
  )@otu_table,
  paste0("data_f", sample_names(data_fungi))
)
#> Taxa are now in rows.
#> Cleaning suppress 0 taxa and 0 samples.
samda <- rename_samples(
  data_fungi@sam_data,
  paste0("data_f", sample_names(data_fungi))
)