Verify Phyloseq Objects before Running the C3NA Pipeline

Source: R/miscFunctions.r

This validation serve to ensure the data are prepared is ready for the C3NA.

  1. Ensure the OTUs/ASVs table, Taxa table and sample data with a diagnosis column present.

  2. The user can provide the correct diagnosis column required for the C3NA phenotype data processing.

validatePhloseq(phyloseqObj = phyloseqObj, diagColName = NA)

Arguments

phyloseqObj

(Required) A phyloseq object.

diagColName

(Optional) Identify the dianogis/phenotype column, and create a 'diagnosis' column the column was named differently.

Value

A phyloseq object

Examples

data(CRC_Phyloseq)
curPhyloseq = validatePhloseq(phyloseqObj = CRC_Phyloseq)