make_design {scone} | R Documentation

## Make a Design Matrix

### Description

This function builds a design matrix for the Adjustment Normalization Step, in which covariates are two (possibly nested) categorical factors and one or more continuous variables.

### Usage

    make_design(bio, batch, W, nested = FALSE)

### Arguments

`bio` | factor. The biological covariate.
`batch` | factor. The batch covariate.
`W` | numeric. Either a vector or matrix containing one or more continuous covariates (e.g. RUVg factors).
`nested` | logical. Whether or not to consider a nested design (see details).

### Details

If nested=TRUE a nested design is used, i.e. the batch variable is assumed to be nested within the bio variable. Here, nested means that each batch is composed of samples from only *one* level of bio, while each level of bio may contain multiple batches.

### Value

The design matrix.

### Examples

    bio = as.factor(rep(c(1,2),each = 2))
    batch = as.factor(rep(c(1,2),2))
    design_mat = make_design(bio,batch, W = NULL)

[Package scone version 1.16.1 Index]