Man pages for MCorentin/vargen
Fetching Variants Related to Phenotypes Using Public Databases
| annotate_variants | Annotate variants from a vector of variant IDs |
| connect_to_gene_ensembl | Connect to gene Mart |
| connect_to_snp_ensembl | Connect to snp Mart |
| convert_gtex_to_rsids | Convert GTEx IDs to rsid |
| create_gwas | Create a gwaswloc object |
| format_chr | Format chromosome names |
| format_output | Format the variants data.frame |
| get_fantom5_enhancers_from_hgnc | Get the enhancers associated to certain genes from FANTOM5 |
| get_fantom5_variants | Get variants on the enhancers of the list of genes given as... |
| get_genes_variants | Get the variants located on the genes |
| get_gtex_variants | Get variants from GTEx linked to the given ensembl genes |
| get_gwas_variants | Get the variants from the gwas catalog associated to the... |
| get_omim_genes | Get ensembl gene IDs from "mim_morbid_accession" |
| get_phenotype_terms | From keywords, get a list of phenotypes to use with snp mart |
| get_variants_from_locations | Using ensembl API to get the variants at certain locations |
| get_variants_from_phenotypes | Get variants associated with certain phenotypes |
| list_gtex_tissues | Generates a vector containing the available GTEx tissue files |
| list_gwas_traits | List the available gwas traits |
| list_omim_accessions | List the available OMIM morbid IDs and descriptions |
| plot_manhattan_gwas | Manhattan plot for variants found in GWAS |
| prepare_fantom | Generate data.frame from FANTOM5 enhancer file |
| select_gtex_tissues | Get the GTEx files corresponding to the tissues of interest |
| vargen_custom | Get variants related to specific genes. |
| vargen_install | Download the files needed to run 'vargen_pipeline' |
| vargen_pipeline | Main vargen function, to get the list of variants |
| vargen_visualisation | Generate a plot of the variants on the OMIM genes |
