constAvBetaTSS: Construct a DNAm matrix at gene-promoter level

In aet21/EpiSCORE: Epigenetic cell-type deconvolution with Single-Cell Omic References

Construct a DNAm matrix at gene-promoter level

Description

This function takes as input a DNAm data matrix generated with Illumina 450k, 850k or EPICv2 technology and outputs a DNAm data matrix at the gene promoter level, by computing the average DNAm over a window 200bp upstream of TSS, or if not available over 1st exon probes.

Usage

constAvBetaTSS(beta.m, type = c("450k", "850k","EPICv2"))

Arguments

type	This specifies whether data is 450k, 850k (EPICv1) or EPICv2.
beta.m	A DNAm beta-valued data matrix with columns labeling samples and rows labeling CpGs. At present we only support Illumina 450k or 850k methylation beadarrays.

Value

The DNAm data matrix at the gene-promoter level.

References

Teschendorff AE, Zhu T, Breeze CE, Beck S. Cell-type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data Genome Biol.2020

Jiao Y, Widschwendter M, Teschendorff AE. A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Bioinformatics (2014) 30(16). doi: 10.1093/bioinformatics/btu316.

Examples

data(testDNAm);
avDNAm.m <- constAvBetaTSS(testDNAm.m,type="450k");

aet21/EpiSCORE documentation built on June 12, 2025, 5:32 p.m.