create_gene_covar_file: Create gene covariance file

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

Create gene covariance file

Description

The gene covariannce (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_gene_covar_file(
  genesOutFile,
  ctd,
  annotLevel,
  ctd_species,
  genesOutCOND = NA,
  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. Must contain quantiles.
annotLevel	Annot level for which the gene covar file should be constructed
ctd_species	Species name relevant to the cell type data, i.e. "mouse" or "human"
genesOutCOND	[Optional] Path to a genes.out file to condition on. Used if you want to condition on a different GWAS.
verbose	Print messages.

Value

File path for the gene covar file.

Source

#### Example usage #### ctd <- ewceData::ctd() genesOutFile <- MAGMA.Celltyping::import_magma_files( ids = "ieu-a-298", file_types = ".genes.out$", return_dir = FALSE) genesCovarFilePath <- MAGMA.Celltyping:::create_gene_covar_file( genesOutFile = genesOutFile, ctd = ctd, annotLevel = 1, ctd_species = "mouse")

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