buildConfMat {RCM} | R Documentation

## A function to build the confounder matrices

### Description

A function to build the confounder matrices

### Usage

    buildConfMat(x, ...)

### Arguments

`x` | a matrix, data frame or character string
`...` | further arguments passed on to other methods For the preliminary trimming, we do not include an intercept, but we do include all the levels of the factors using contrasts=FALSE: we want to do the trimming in every subgroup, so no hidden reference levels For the filtering we just use a model with an intercept and treatment coding, here the interest is only in adjusting the offset

### Value

a list with components

`confModelMatTrim` | A confounder matrix without intercept, with all levels of factors present. This will be used to trim out taxa that have zero abundances in any subgroup defined by confounders
`confModelMat` | A confounder matrix with intercept, and with reference levels for factors absent. This will be used to fit the model to modify the independence model, and may include continuous variables

[Package RCM version 1.3.0 Index]