Man pages for NathanSkene/MAGMA_Celltyping
Find Causal Cell-Types Underlying Complex Trait Genetics
| adjust_zstat_in_genesOut | Adjust MAGMA Z-statistic from _.genes.out_ files |
| build_snp_location_tables | Build SNP location tables |
| 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 |
| capture | Capture output of function |
| celltype_associations_pipeline | Calculate cell type associations using MAGMA |
| check_access | Check access |
| check_controlledCTs | Check controlled cell type names |
| check_enrichment_mode | Check enrichment mode |
| check_entrez_genes | Check ENTREZ genes |
| check_inputs_to_magma_celltype_analysis | Check input to MAGMA cell type analyses |
| check_quantiles | Check quantiles |
| compare_trait_enrichments | Test to see which cell types are more enriched in magmaPath2... |
| copy_snps_to_genes_files | Copy MAGMA gene mapping files to new folder |
| create_DT | Create data table |
| create_fake_gwas_path | Create a fake GWAS path when all you have are the MAGMA files |
| create_gene_covar_file | Create gene covariance file |
| create_gene_covar_file_mode | Create gene covariance file: by mode |
| create_genesets | Create gene sets |
| create_top10percent_genesets_file | Create gene covar file |
| decompress | Decompress a file |
| drop_genes_within_mhc | Drop genes within MHC |
| enrichment_results | Example celltype enrichment results |
| filter_by_orthologs | Filter CellTypeDataset |
| find_GenesOut_files | Find genes.out files |
| find_install_dir | Find a directory to install software in |
| fix_celltype_names2 | Fix celltype names |
| fix_path | Fix path |
| format_sumstats_for_magma | Format GWAS summary statistics |
| format_sumstats_for_magma_macOnly | Check that sumstats has correct columns and that they are in... |
| get_actual_path | Get actual path |
| get_ctd | Import precomputed CellTypeDatasets |
| get_ctd_dendro | Get CTD dendro |
| get_data | Get remote data |
| get_deciles_matrix | Get deciles matrix |
| get_driver_genes | Get genes driving significant 'MAGMA_celltyping' results |
| get_example_gwas | Import GWAS summary statistics |
| get_example_gwas_raw | Example GWAS: raw (pre-munged) |
| get_example_magma_files | Get example MAGMA files |
| get_gene_info | Get gene info |
| get_genomebuild_for_sumstats | Get genome build for sumstats |
| get_genomeLocFile | Import gene location files |
| get_genome_ref | Download genome ref |
| get_genome_ref_magma | Download genome ref: magma |
| get_genome_ref_piggyback | Download genome ref: piggyback |
| get_magma_paths | Get MAGMA Paths |
| get_os | Get OS |
| get_sub_SNP_LOC_DATA | Download genome ref: piggyback |
| github_download_files | Download files from GitHub |
| github_list_files | List files |
| gwas_munged | Munged GWAS |
| hgnc2entrez_orthogene | HGNC to Entrez symbol mapping |
| import_magma_files | Import preprocessed MAGMA files |
| import_magma_files_metadata | Import MAGMA files metadata |
| import_magma_files_tables | Import magma files as tables |
| infer_ctd_species | Infer CellTypeDataset species |
| infer_geneset_species | Infer gene set species |
| invert_dict | Invert dictionary |
| is_32bit | Checks whether OS is a 32-bit Windows |
| iterate_conditional_celltypes | iterate_conditional_celltypes |
| iterate_conditional_celltypes_grouped | iterate_conditional_celltypes: grouped |
| list_remote_files | List files |
| list_snps_to_genes_files | List SNPs-to-genes mapping files |
| load_magma_results_file | Load a MAGMA .gcov.out file |
| load_rdata | Load RData |
| load_snp_loc_data | Downloads and loads the SNP_LOC_DATA file that I stashed at... |
| magma_check | MAGMA check |
| magma_check_version_match | MAGMA check version match |
| magma_download_binary | Download a MAGMA binary |
| magma_executable | Find the local executable |
| magma_executable_select | Select a MAGMA executable |
| magma_files_metadata | MAGMA_Files_Public: metadata |
| magma_find_executable | Find MAGMA executable |
| magma_install | Install the MAGMA command line tool |
| magma_installed | MAGMA installed |
| magma_installed_version | MAGMA installed version |
| magma_links | Get MAGMA links |
| magma_links_gather | Gather MAGMA links |
| magma_links_query | Query MAGMA links |
| magma_links_stored | Stored links to MAGMA executables |
| magma_links_versions | Get MAGMA versions |
| magma_os_suffix | Get MAGMA OS suffix |
| magma_read_covar_out | MAGMA: read gsa.out |
| magma_read_sets_out | MAGMA: read sets.out |
| magma_run | Run MAGMA |
| magma_tileplot | MAGMA tile plot |
| magma_uninstall | Uninstall MAGMA |
| map_snps_to_genes | Map SNPs to their nearby genes |
| map_specificity_to_entrez | Map specificity to Entrez gene IDs |
| merge_magma_results | Merge MAGMA results |
| merge_results | Gather enrichment results |
| message_parallel | Message parallel |
| messager | Print messages |
| mungesumstats_deprecation_msg | Deprecation notice |
| plot_celltype_associations | Plot celltype associations calculated using MAGMA |
| prepare_quantile_groups | Prepare quantile groups for each celltype based on... |
| rbfox_binding | Rbfox binding genes in MGI format |
| read_magma_genes_out | Read a _.genes.out_ file |
| read_magma_genes_raw | Read a _.genes.raw_ file |
| results_heatmap | Plot heatmap of enrichment results |
| set_permissions | Set permissions |
| standardise.sumstats.column.headers | Standardise the column headers in the Summary Statistics... |
| standardise.sumstats.column.headers.crossplatform | Standardise the column headers in the Summary Statistics... |
