mbecProcessInput-phyloseq-method: Mbec-Data Constructor Wrapper

In buschlab/MBECS: Evaluation and correction of batch effects in microbiome data-sets

Description

This function is a wrapper for the constructor of MbecData-objects from phyloseq objects and lists of counts and sample data.

Usage

## S4 method for signature 'phyloseq'
mbecProcessInput(input.obj, required.col = NULL)

Arguments

input.obj	One of MbecData, phyloseq or list(counts, meta-data).
required.col	Vector of column names that need to be present in the meta-data table.

Details

The (OPTIONAL) argument 'required.col' is a vector of column-names that will enable a sanity test for the presence in the meta-data table. Which is also the second use-case for objects that are already of class MbecData.

Value

An object of type MbecData that has been validated.

Examples

# This will check for the presence of variables 'group' and 'batch' in the
# meta-data and return an object of class 'MbecData'.
MbecData.obj <- mbecProcessInput(input.obj=dummy.mbec,
    required.col=c("group","batch"))

buschlab/MBECS documentation built on Jan. 21, 2022, 1:27 a.m.