Trans_from_microeco: Convert a microeco object to a LorMe object

In LorMe: Lightweight One-Line Resolving Microbial Ecology Program

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
)

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

Value

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

Note

For taxonomy annotation with both 'Domain' and 'Kingdom' level, please set 'into' parameter as 'complete'!!!

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
}

LorMe documentation built on Jan. 12, 2026, 9:06 a.m.