MIND.md

In randel/MIND: Using Tissue Expression to Estimate Sample-/Subject- And Cell-Type-Specific Gene Expression via Deconvolution

MIND: using multiple measurements of tissue to estimate subject-and cell-type-specific gene expression

Example

Estimate subject- and cell-type-specific gene expression (saved as deconv$A below) using bulk gene expression data and pre-estimated cell type fractions:

• X: bulk gene expression (gene x subject x measure)
• W: cell type fraction (subject x measure x cell type)

library(MIND)

data(example)

deconv = mind(X = example$X, W = example$W)

For details, please see the PDF manual.

The cell type fraction can be pre-estimated using est_frac() (based on non-negative least squares, see an example here) or another standard deconvolution method. It requires a signature matrix derived from reference samples of single-cell RNA-seq data.

Reference

MIND: Wang, Jiebiao, Bernie Devlin, and Kathryn Roeder. "Using multiple measurements of tissue to estimate subject-and cell-type-specific gene expression." Bioinformatics 36.3 (2020): 782-788. https://doi.org/10.1093/bioinformatics/btz619

randel/MIND documentation built on May 6, 2023, 7:45 a.m.