create_top10percent_genesets_file: Create gene covar file

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

Create gene covar file

Description

The gene covar file is the input to MAGMA for the celltype association analysis. This code was functonalised because it is called by both baseline and conditional analysis.

Usage

create_top10percent_genesets_file(
  genesOutFile,
  ctd,
  annotLevel,
  ctd_species,
  verbose = TRUE
)

Arguments

genesOutFile	The output of the second call to MAGMA (performed in the map_snps_to_genes function).
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.
verbose	Print messages.

Value

Filepath for the gene covar file

Source

#### Prepare cell-type data #### ctd <- ewceData::ctd() #### Prepare GWAS MAGMA data #### myGenesOut <- MAGMA.Celltyping::import_magma_files(ids = "ieu-a-298", file_types = ".genes.out", return_dir = FALSE) ctd <- MAGMA.Celltyping::prepare_quantile_groups(ctd = ctd) geneSetsFilePath <- MAGMA.Celltyping:::create_top10percent_genesets_file( genesOutFile = myGenesOut, ctd = ctd, annotLevel = 1, ## Mapped to human orths by prepare_quantile_groups previously ctd_species = "human" )

NathanSkene/MAGMA_Celltyping documentation built on March 5, 2025, 5:44 a.m.