ImputeDNAmRef: Impute a DNAm reference matrix

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

Impute a DNAm reference matrix

Description

This function takes as input a mRNA expression reference matrix and will generate an imputed DNAm reference using one of two databases (NIH Epigenomics Roadmap or Stem-Cell Matrix Compendium) specified by the user.

Usage

ImputeDNAmRef(
  refexp.m,
  db = c("SCM2", "RMAP"),
  geneID = c("SYMBOL", "ENTREZID")
)

Arguments

refexp.m	The gene expression reference matrix with rows labeling genes and columns labeling cell-types. If gene idgentifier is gene symbol this will be converted to Entrez gene ID.
db	A character specifying the database of matched expression and DNAm data. This has to be either SCM2 for Stem-Cell-Matrix Compendium-2 or RMAP for Epigenomics Roadmap.
geneID	A character specifying gene identifier used in expression reference matrix input. Either SYMBOL or ENTREZ GENE ID.

Value

The imputed DNAm reference matrix defined over the same cell-types as defined in the input expression 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));
refDNAm.m <- ImputeDNAmRef(out.l$ref$med,db="SCM2",geneID="SYMBOL");
print(head(refDNAm.m));

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