buildConfMat: A function to build the confounder matrices

In RCM: Fit row-column association models with the negative binomial distribution for the microbiome

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

RCM documentation built on Nov. 8, 2020, 5:22 p.m.