ConstMergedDNAmRef: Construct merged DNAm reference matrix

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

Construct merged DNAm reference matrix

Description

This function takes as input two separate imputed DNAm reference matrices and merges them to arrive at a unique final DNAm reference matrix.

Usage

ConstMergedDNAmRef(ref1.m, ref2.m)

Arguments

ref1.m	The first DNAm reference matrix, say generated from the SCM2 database
ref2.m	The second DNAm reference matrix, say generated from the RMAP database

Value

The merged DNAm reference matrix

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

Zhu T, Liu J, Beck S, Pan S, Capper D, Lechner M, Thirlwell C, Breeze CE, Teschendorff AE. A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution Nat Methods 2022

Examples

data(lungSS2mca1)
out.l <- ConstExpRef(lungSS2mca1.m,celltypeSS2.idx,celltypeSS2.v,markspecTH.v=rep(3,4));
refDNAm1.m <- ImputeDNAmRef(out.l$ref$med,db="SCM2",geneID="SYMBOL");
refDNAm2.m <- ImputeDNAmRef(out.l$ref$med,db="RMAP",geneID="SYMBOL");
refDNAm.m <- ConstMergedDNAmRef(refDNAm1.m,refDNAm2.m);
print(head(refDNAm.m));

aet21/EpiSCORE documentation built on June 26, 2022, 5:50 p.m.