Function reference • MAGMA.Celltyping

All functions
`adjust_zstat_in_genesOut()`	Adjust MAGMA Z-statistic from .genes.out files
`calculate_celltype_associations()`	Calculate celltype associations using MAGMA
`calculate_celltype_enrichment_limma()`	Calculate celltype enrichment
`calculate_conditional_celltype_associations()`	Calculate conditional celltype associations using MAGMA
`calculate_conditional_celltype_enrichment_limma()`	Calculate celltype enrichments without MAGMA
`calculate_conditional_geneset_enrichment()`	Use MAGMA to test enrichment in a geneset
`calculate_geneset_enrichment()`	Use MAGMA to test enrichment in a geneset
`celltype_associations_pipeline()`	Calculate cell type associations using MAGMA
`compare_trait_enrichments()`	Test to see which cell types are more enriched in magmaPath2 than magmaPath1
`create_DT()`	Create data table
`drop_genes_within_mhc()`	Drop genes within MHC
`enrichment_results`	Example celltype enrichment results
`format_sumstats_for_magma()`	Format GWAS summary statistics
`get_ctd()`	Import precomputed CellTypeDatasets
`get_driver_genes()`	Get genes driving significant MAGMA_celltyping results
`get_example_gwas()`	Import GWAS summary statistics
`get_genome_ref()`	Download genome ref
`get_genomebuild_for_sumstats()`	Get genome build for sumstats
`get_magma_paths()`	Get MAGMA Paths
`gwas_munged`	Munged GWAS
`hgnc2entrez_orthogene`	HGNC to Entrez symbol mapping
`import_magma_files()`	Import preprocessed MAGMA files
`infer_ctd_species()`	Infer CellTypeDataset species
`infer_geneset_species()`	Infer gene set species
`list_snps_to_genes_files()`	List SNPs-to-genes mapping files
`load_magma_results_file()`	Load a MAGMA .gcov.out file
`magma_files_metadata`	MAGMA_Files_Public: metadata
`magma_install()`	Install the MAGMA command line tool
`magma_links_stored`	Stored links to MAGMA executables
`magma_run()`	Run MAGMA
`magma_tileplot()`	MAGMA tile plot
`magma_uninstall()`	Uninstall MAGMA
`map_snps_to_genes()`	Map SNPs to their nearby genes
`merge_magma_results()`	Merge MAGMA results
`merge_results()`	Gather enrichment results
`plot_celltype_associations()`	Plot celltype associations calculated using MAGMA
`prepare_quantile_groups()`	Prepare quantile groups for each celltype based on specificity
`rbfox_binding`	Rbfox binding genes in MGI format
`results_heatmap()`	Plot heatmap of enrichment results
`standardise.sumstats.column.headers()`	Standardise the column headers in the Summary Statistics files

Reference

All functions