read_pq: Read phyloseq object from multiple csv tables and a...

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Read phyloseq object from multiple csv tables and a phylogenetic tree in Newick format.

Description

This is the reverse function of write_pq().

Usage

read_pq(
  path = NULL,
  taxa_are_rows = FALSE,
  sam_names = NULL,
  sep_csv = "\t",
  ...
)

Arguments

path	(required) a path to the folder to read the phyloseq object
taxa_are_rows	(default to FALSE) see ?phyloseq for details
sam_names	The name of the variable (column) in sam_data.csv to rename samples. Note that if you use write_phyloseq() function to save your physeq object, you may use sam_names = "X" to rename the samples names as before.
sep_csv	(default tabulation) separator for column
...	Other arguments passed on to utils::write.table() function.

Value

One to four csv tables (refseq.csv, otu_table.csv, tax_table.csv, sam_data.csv) and if present a phy_tree in Newick format. At least the otu_table.csv need to be present.

Examples

write_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"))
read_pq(path = paste0(tempdir(), "/phyloseq"))
unlink(paste0(tempdir(), "/phyloseq"), recursive = TRUE)

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.