metapr2_export_asv: Exports the metapr2 database
In vaulot/dvutils: A set of utilities

Description Usage Arguments Value Examples

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

metapr2_export_asv(
  taxo_level = kingdom,
  taxo_name = "Eukaryota",
  boot_level = class_boot,
  boot_min = 0,
  assigned_with = "dada2",
  reference_database = "pr2_4.14.0",
  directory = "C:/daniel.vaulot@gmail.com/Databases/_metaPR2/export/",
  dataset_id_selected = c(1:500),
  filter_samples = NULL,
  filter_metadata = NULL,
  export_long_xls = FALSE,
  export_wide_xls = FALSE,
  export_sample_xls = FALSE,
  export_phyloseq = FALSE,
  export_fasta = FALSE,
  taxonomy_full = TRUE,
  use_hash = FALSE,
  sum_reads_min = 0
)

`taxo_level`	The taxonomic level for selection (do not quote), e.g. class or genus
`taxo_name`	The name of the taxonomic level selected, e.g. "Chlorophyta", can be a vector c("Chlorophyta", "Haptophyta")
`boot_level`	The taxonomic level for bootstrap filtering (do not quote), e.g. class_boot or genus_boot
`boot_min`	Minimum bootstrap value at the class level, 0 if you want to get all asvs
`assigned_with`	Program used for assignement - "dada2" or "decipher"
`reference_database`	Reference database used - "pr2_4.14.0" or "pr2_4.12.0"
`directory`	Directory where the files are saved (finish with /)
`dataset_id_selected`	Integer vector, e.g. 23 or c(21, 23) or 21:23
`filter_samples`	Character expression for filter, e.g. "DNA_RNA == 'DNA'" (use single quotes inside double quotes)
`filter_metadata`	Character expression for filter, e.g. "substrate == 'sediment trap material'" (use single quotes inside double quotes)
`export_long_xls`	If TRUE, an xlsx file is produced containing the final long data frame
`export_wide_xls`	If TRUE, an xlsx file is produced containing the final wide data frame
`export_sample_xls`	If TRUE, an xlsx file is produced containing the sample list
`export_phyloseq`	If TRUE, a phyloseq file is produced and a phyloseq object producted
`export_fasta`	If TRUE, a fasta is produced
`taxonomy_full`	If TRUE, the fasta file contains the full taxonomy (8 levels), if false only contains the species
`use_hash`	If TRUE, the asvs with identical has will be merged and called by their hash value (sequence_hash)
`sum_reads_min`	This is the minimum number of reads (summed over the datasets selected) for an asv to be included

A list with 4 elements

# Export all the asv in a single fasta
  metapr2_export_asv()

# Export as specific data set as a phyloseq file
  metapr2_export_asv(dataset_id_selected = 23, export_phyloseq = TRUE)

# Export a specific genus as a fasta file and an excel file
  asv_set <- metapr2_export_asv(taxo_level = genus, taxo_name=c("Pseudohaptolina","Haptolina"),
                                export_fasta=TRUE, taxonomy_full= FALSE,
                                boot_level = genus_boot, boot_min = 100,
                                export_long_xls = TRUE)