download_ref: Download functional prediction reference tables

Description Usage Arguments See Also Examples

View source: R/download_ref.R

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

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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

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

## End(Not run)

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