Man pages for NathanSkene/MAGMA_Celltyping
Find Causal Cell-Types Underlying Complex Trait Genetics

adjust_zstat_in_genesOutAdjust MAGMA Z-statistic from _.genes.out_ files
build_snp_location_tablesBuild SNP location tables
calculate_celltype_associationsCalculate celltype associations using MAGMA
calculate_celltype_enrichment_limmaCalculate celltype enrichment
calculate_conditional_celltype_associationsCalculate conditional celltype associations using MAGMA
calculate_conditional_celltype_enrichment_limmaCalculate celltype enrichments without MAGMA
calculate_conditional_geneset_enrichmentUse MAGMA to test enrichment in a geneset
calculate_geneset_enrichmentUse MAGMA to test enrichment in a geneset
captureCapture output of function
celltype_associations_pipelineCalculate cell type associations using MAGMA
check_accessCheck access
check_controlledCTsCheck controlled cell type names
check_enrichment_modeCheck enrichment mode
check_entrez_genesCheck ENTREZ genes
check_inputs_to_magma_celltype_analysisCheck input to MAGMA cell type analyses
check_quantilesCheck quantiles
compare_trait_enrichmentsTest to see which cell types are more enriched in magmaPath2...
copy_snps_to_genes_filesCopy MAGMA gene mapping files to new folder
create_DTCreate data table
create_fake_gwas_pathCreate a fake GWAS path when all you have are the MAGMA files
create_gene_covar_fileCreate gene covariance file
create_gene_covar_file_modeCreate gene covariance file: by mode
create_genesetsCreate gene sets
create_top10percent_genesets_fileCreate gene covar file
decompressDecompress a file
drop_genes_within_mhcDrop genes within MHC
enrichment_resultsExample celltype enrichment results
filter_by_orthologsFilter CellTypeDataset
find_GenesOut_filesFind genes.out files
find_install_dirFind a directory to install software in
fix_celltype_names2Fix celltype names
fix_pathFix path
format_sumstats_for_magmaFormat GWAS summary statistics
format_sumstats_for_magma_macOnlyCheck that sumstats has correct columns and that they are in...
get_actual_pathGet actual path
get_ctdImport precomputed CellTypeDatasets
get_ctd_dendroGet CTD dendro
get_dataGet remote data
get_deciles_matrixGet deciles matrix
get_driver_genesGet genes driving significant 'MAGMA_celltyping' results
get_example_gwasImport GWAS summary statistics
get_example_gwas_rawExample GWAS: raw (pre-munged)
get_example_magma_filesGet example MAGMA files
get_gene_infoGet gene info
get_genomebuild_for_sumstatsGet genome build for sumstats
get_genomeLocFileImport gene location files
get_genome_refDownload genome ref
get_genome_ref_magmaDownload genome ref: magma
get_genome_ref_piggybackDownload genome ref: piggyback
get_magma_pathsGet MAGMA Paths
get_osGet OS
get_sub_SNP_LOC_DATADownload genome ref: piggyback
github_download_filesDownload files from GitHub
github_list_filesList files
gwas_mungedMunged GWAS
hgnc2entrez_orthogeneHGNC to Entrez symbol mapping
import_magma_filesImport preprocessed MAGMA files
import_magma_files_metadataImport MAGMA files metadata
import_magma_files_tablesImport magma files as tables
infer_ctd_speciesInfer CellTypeDataset species
infer_geneset_speciesInfer gene set species
invert_dictInvert dictionary
is_32bitChecks whether OS is a 32-bit Windows
iterate_conditional_celltypesiterate_conditional_celltypes
iterate_conditional_celltypes_groupediterate_conditional_celltypes: grouped
list_remote_filesList files
list_snps_to_genes_filesList SNPs-to-genes mapping files
load_magma_results_fileLoad a MAGMA .gcov.out file
load_rdataLoad RData
load_snp_loc_dataDownloads and loads the SNP_LOC_DATA file that I stashed at...
magma_checkMAGMA check
magma_check_version_matchMAGMA check version match
magma_download_binaryDownload a MAGMA binary
magma_executableFind the local executable
magma_executable_selectSelect a MAGMA executable
magma_files_metadataMAGMA_Files_Public: metadata
magma_find_executableFind MAGMA executable
magma_installInstall the MAGMA command line tool
magma_installedMAGMA installed
magma_installed_versionMAGMA installed version
magma_linksGet MAGMA links
magma_links_gatherGather MAGMA links
magma_links_queryQuery MAGMA links
magma_links_storedStored links to MAGMA executables
magma_links_versionsGet MAGMA versions
magma_os_suffixGet MAGMA OS suffix
magma_read_covar_outMAGMA: read gsa.out
magma_read_sets_outMAGMA: read sets.out
magma_runRun MAGMA
magma_tileplotMAGMA tile plot
magma_uninstallUninstall MAGMA
map_snps_to_genesMap SNPs to their nearby genes
map_specificity_to_entrezMap specificity to Entrez gene IDs
merge_magma_resultsMerge MAGMA results
merge_resultsGather enrichment results
message_parallelMessage parallel
messagerPrint messages
mungesumstats_deprecation_msgDeprecation notice
plot_celltype_associationsPlot celltype associations calculated using MAGMA
prepare_quantile_groupsPrepare quantile groups for each celltype based on...
rbfox_bindingRbfox binding genes in MGI format
read_magma_genes_outRead a _.genes.out_ file
read_magma_genes_rawRead a _.genes.raw_ file
results_heatmapPlot heatmap of enrichment results
set_permissionsSet permissions
standardise.sumstats.column.headersStandardise the column headers in the Summary Statistics...
standardise.sumstats.column.headers.crossplatformStandardise the column headers in the Summary Statistics...
NathanSkene/MAGMA_Celltyping documentation built on Oct. 11, 2024, 7:19 a.m.