makeDesign: Generate design matrix from input phenotypes and proportions.

In ziyili20/TOAST: Tools for the analysis of heterogeneous tissues

Generate design matrix from input phenotypes and proportions.

Description

This function generate design matrix and make preparations for following fitModel and csTest.

Usage

makeDesign(design, Prop)

Arguments

design	A N by P phenotype matrix, with rows as samples and columns as phenotypes (e.g. age, gender, disease, etc.).
Prop	A N by K proportion matrix, with rows as samples and columns as cell types

Value

design_matrix	A comprehensive design matrix incorporated phenotype and proportion information.
Prop	The input proportion matrix.
design	The input design/phenotype matrix.
all_coefs	The names of all phenotypes.
all_cell_types	The names of all cell types.
formula	The formula of the tested model, including all phenotypes, cell types and interaction terms.

Author(s)

Ziyi Li <[e-mail]>

References

Ziyi Li, Zhijin Wu, Peng Jin, Hao Wu. "Dissecting differential signals in high-throughput data from complex tissues."

Examples

N = 300 # simulation a dataset with 300 samples
K = 3 # 3 cell types

### simulate proportion matrix
Prop = matrix(runif(N*K, 10,60), ncol=K)
Prop = sweep(Prop, 1, rowSums(Prop), FUN="/")
colnames(Prop) = c("Neuron", "Astrocyte", "Microglia")

### simulate phenotype names
design <- data.frame(disease=factor(sample(0:1, size = N,replace=TRUE)),
                     age=round(runif(N, 30,50)),
                     race=factor(sample(1:3, size = N,replace=TRUE)))
Design_out <- makeDesign(design, Prop)

ziyili20/TOAST documentation built on Aug. 28, 2022, 11:28 a.m.