saveData: Save data

In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

Save data

Description

Save data

Usage

saveAbundanceData(
  x,
  path_file = NULL,
  file_type = c("delim", "csv", "csv2", "tsv", "excel_csv", "excel_csv2"),
  ...
)

saveTaxonomyData(
  x,
  path_file = NULL,
  file_type = c("delim", "csv", "csv2", "tsv", "excel_csv", "excel_csv2"),
  ...
)

saveSampleData(
  x,
  path_file = NULL,
  file_type = c("delim", "csv", "csv2", "tsv", "excel_csv", "excel_csv2"),
  ...
)

Arguments

x	phyloseq object
path_file	path to save the file along with name. Default is NULL. E.g. "data/output/otu_table.csv"
file_type	One of "delim","csv","csv2","tsv","excel_csv","excel_csv2" supported by readr package
...	Arguments to pass to readr functions

Details

Basic utilities for saving data in phyloseq.

saveAbundanceData save the otu_table.

saveTaxonomyData save the taxa_table.

saveSampleData save the sample_data.

Value

Store file locally specified by user.

Author(s)

Sudarshan A. Shetty

References

Shetty SA (2020). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils

Examples

## Not run: 
library(biomeUtils)
data("FuentesIliGutData")
saveAbundanceData(FuentesIliGutData, path_file = "otu.tsv", file_type = "tsv")
saveTaxonomyData(FuentesIliGutData, path_file = "taxa.tsv", file_type = "tsv")
saveSampleData(FuentesIliGutData, path_file = "sample.tsv", file_type = "tsv")

## End(Not run)

RIVM-IIV-Microbiome/biomeUtils documentation built on July 20, 2023, 10:29 a.m.