map_specificity_to_entrez: Map specificity to Entrez gene IDs

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Map specificity to Entrez gene IDs

Description

Convenience function used in create_gene_covar_file.

Usage

map_specificity_to_entrez(
  ctd,
  annotLevel,
  ctd_species,
  use_matrix = "specificity_quantiles",
  return_ctd = FALSE,
  use_saved = TRUE,
  verbose = TRUE
)

Arguments

ctd	Cell type data structure containing specificity_quantiles.
ctd_species	Species name relevant to the CellTypeDataset (ctd). See list_species for all available species. If ctd_species=NULL (default), the ctd species will automatically be inferred using infer_species.
use_matrix	Which CTD matrix to use as input.
return_ctd	Return the actual CellTypeDataset, rather than path to where it is saved.
use_saved	Use a saved version of the gene mapping table.
verbose	Print messages.

Value

Matrix in which the first column is 'entrez' and then the specificity decile for each cell type

NathanSkene/MAGMA_Celltyping documentation built on Aug. 21, 2023, 8:55 a.m.