get_sig

Generate Deconvolution Signatures

This function generates deconvolution signatures based on the provided parameters. It uses differentially methylated CpG sites from single-cell DNA methylation (scDNAm) data to identify markers for various cell types.

get_sig(
  nmrk,
  sig = sig_all,
  DM_df = Mrk_twosided,
  ct_ind = c("Astro", "Micro", "Neuro", "Oligo")
)

Arguments

nmrk

An integer specifying the number of marker CpG sites to consider for each cell type.

DM_df

A data frame detailing differentially methylated CpG sites from scDNAm data. It should include columns for TargetID and celltype_ind, where columns corresponding to celltype_ind should have p-values for each cell type.

ct_ind

A character vector listing the cell types to include in the analysis. Default is c("Astro","Micro", "Neuro","Oligo").

beta_mtx

A matrix representing the scDNAm data, CpG sites by cell types. Default is NULL. If NULL, the function will utilize the inbuilt scDNAm dataset.

Value

A matrix of signatures that can be used for deconvolution, CpG sites by cell types.