metapr2_export_qs: Exports the metapr2 database in qs file for shiny app

In vaulot/dvutils: A set of utilities

Description

Exports a range of file and format.

• fasta file with the full taxonomy or just the genus level

• excel file with the full table of the asv and metadata

• phyloseq file (better when only selecting a single data set)

• list of samples with metadata

Returns a list with 4 elements

• df = dataframe with all the asv and the stations and read numbers

• ps = phyloseq object - if phyloseq = TRUE

• fasta = df with 2 columns seq_name and sequence

• samples= sample_list (list of sammples with metadata)

NOTE: if all export_long_xls, export_wide_xls, export_phyloseq are false, abundances are not exported

Usage

metapr2_export_qs(set_type = "public", directory = "data/")

Arguments

set_type	"public" (41 sets), "basic" (5 sets only), "all"
directory	Directory where the files are saved (finish with /)

Value

TRUE if successful

Examples

# Export public data set

  metapr2_export_qs("public")

vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.