LorMe (version 2.0.1)

Trans_from_microeco: Convert a microeco object to a LorMe object

Description

Convert a microeco object to a LorMe object

Usage

Trans_from_microeco(
  microtab,
  into = "standard",
  outputtax = c("Phylum", "Genus"),
  reads = TRUE
)

Value

LorMe object containing taxonomy table data frame,containing reads and percentage table for each specified output.

Arguments

microtab

A microtable object

into

Names of separated taxonomy to create as character vector. Must select from c("Domain","Phylum","Class","Order","Family","Genus","Species"). Shortcut input:1)By default."standard":c("Domain","Phylum","Class","Order","Family","Genus","Species"). Used for standard taxonomy annotation to OTU/ASV table. 2)"complete":c("Domain","Kingdom","Phylum","Class","Order","Family","Genus","Species"). Used for complete taxonomy annotation to meta genomic table.

outputtax

Default:c("Phylum","Genus").Names of output taxonomy level table. Shortcut input is available with 'standard' and 'complete' same as above.

reads

Logical.True for reads table and FALSE for percentage table. Default: TRUE

Examples

## Not run:
if (requireNamespace("microeco", quietly = TRUE)) {
 data("dataset", package = "microeco")

 ## convert microeco object to LorMe format
 dataset_obj <- Trans_from_microeco(dataset, outputtax = "standard")

 ## specify experimental design
 dataset_obj_plan <- object_config(dataset_obj,
                          treat_location = 4)

 ## generate community-structure PCoA plot (Genus level)
 community_structure <- structure_plot(dataset_obj_plan, taxlevel = "Genus")
 community_structure$PCoA_Plot
}