This function loads and returns the X_cibersort reference matrix used for cell type deconvolution with the Cibersort and LLSR methods. The reference matrix contains gene expression signatures for 22 immune cell types.
get_X_cibersort()The X_cibersort reference matrix with genes as rows and cell types as columns
Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., Hoang, C. D., Diehn, M., & Alizadeh, A. A. (2015). Robust enumeration of cell subsets from tissue expression profiles. Nature Methods, 12(5), 453-457. doi:10.1038/nmeth.3337
# Get the default Cibersort reference matrix
ref_matrix <- get_X_cibersort()
# Use with deconvolve_cellularity
# se |> deconvolve_cellularity(reference = get_X_cibersort(), method = "cibersort")