Object handler

A function that handles the conversion of objects to metacoder (taxa::taxmap) objects.

object_handler(obj)

Arguments

obj	An object that contains the data being analyzed. Can be one of the following: Phyloseq Object An object generated from the phyloseq package. Taxmap Object An object generated from the metacoder or taxa package. RData file An RData file generated from the base::save function. Can have an extension of .RData or .rda.

Value

The output generated is a taxa::taxmap object.

Details

This function is used to convert data to metacoder/taxmap objects for microbiome analysis. This function is used at the beginning of every other function to support multiple types of input for the obj parameter in those functions.

See also

parse_phyloseq

fileutils

Other Validation: is_analyzed_format, is_basic_format, is_phyloseq_format, is_raw_format, order_metacoder_data, validate_MicrobiomeR_format, which_format

Examples

# NOT RUN {
if(interactive()){
 library(MicrobiomeR)
 phy_obj <- MicrobiomeR::phyloseq_silva_2
 mc_obj <- object_handler(phy_obj)
 }
# }