download_ref: Download functional prediction reference tables

In EESI/themetagenomics: Exploring Thematic Structure and Predicted Functionality of 16s rRNA Amplicon Data

Description

A function to download the KO and COG 13.5 GreenGenes reference tables for PICRUSt prediction or the KO reference table for tax4fun prediction. The data are stored at https://gitlab.com/sw1/themetagenomics_data/.

Usage

download_ref(
  destination,
  reference = c("all", "gg_ko", "gg_cog", "silva_ko"),
  overwrite = FALSE,
  verbose = FALSE
)

Arguments

destination	Location of the folder to save the reference files.
reference	A string for either gg_ko, gg_cog, silva_ko, or all. Defaults to all.
overwrite	Logical flag to overwrite if file already exists. Default to FALSE.
verbose	Logical flag to print progress information. Defaults to FALSE.

See Also

picrust t4f

Examples

## Not run: 
download_ref(destination='/references',reference='gg_ko')

## End(Not run)

EESI/themetagenomics documentation built on May 10, 2020, 1:40 a.m.