run meth_atlas
Usage
run_meth_atlas(
beta_matrix,
reference_atlas = system.file("reference_atlas.csv", package = "methylDeconv"),
temp_dir = NULL,
out_dir = NULL,
use_epic_reference = FALSE
)Arguments
- reference_atlas
Path to a csv file that saves a reference matrix with CpGs as rows and cell types as columns. The default (tissue-wide) reference file is stored in 'inst/reference_atlas.csv'.
- temp_dir
Path to directory where the beta matrix will be saved as a csv file.
- out_dir
Path to output directory. Output will be a csv file and a png representing the cell type fractions.
- use_epic_reference
The MethAtlas has a whole-tissue reference or a immunecell-specific reference that is optimized for EPIC arrays (which is a subset of the whole-tissue reference)
- methyl_set
A minfi MethylSet