Package index • 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_barplot(): Plot barplot of enrichment results - plotting -log10 (p-value) but cut-off significance is based on FDR where if either linear or top10 FDR threshold the result will be plotted
results_heatmap(): Plot heatmap of enrichment results
standardise.sumstats.column.headers(): Standardise the column headers in the Summary Statistics files