make_design: Make a Design Matrix

In YosefLab/scone: Single Cell Overview of Normalized Expression data

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)

YosefLab/scone documentation built on Oct. 21, 2024, 4:39 p.m.