Man pages for svenstringer/genematrix
Create a Table with Gene Annotation and Output in Convenient Format
| add_annotations | Add annotations to core gene matrix |
| add_to_symbol_table | Symbol |
| annotate_magma | Create gene annotation file for MAGMA (and install MAGMA if... |
| check_path | Checks if path exists |
| compute_genebased_p | Compute gene-based pvalue based on daner summary stats file |
| compute_genebased_pvalues | Compute gene-based pvalue based on daner summary stats files... |
| create_core_matrix | Core matrix is a merge between gencode, entrez and hgnc data. |
| create_dir | Create directory if it does not exist |
| create_symbol_table | Create gene symbol translation table |
| download_source | Download source url if it does not exist in destination path |
| generate_genematrix | Save annotated Gene Matrix |
| get_core_matrix | Load core gene matrix and create it first if it does not... |
| get_magma_osversion | Get compiled magma platform version to download: windows... |
| get_symbol_table | Load gene name translation table and create if it does not... |
| gm_settings | symbol','aliases','strand','merge_trial',... |
| install_magma | Install stand-alone magma if not available yet |
| is_par | Check whether a genomic position is in a PAR regions Assumes... |
| lookup_symbol | Lookup gene symbol in gene-translation-table (gtt) |
| merge_annotation_by_genename | Merge processed annotation file to gene matrix |
| merge_commonmindDLPFC | Merge omim phenotypes to gene matrix |
| merge_core_entrez | Merge gencode and hgnc file |
| merge_exacpli | Merge exac pli constraint data into gene matrix |
| merge_gencode_hgnc | Merge gencode and hgnc file |
| merge_genebased_pvalues | Compute gene-based pvalue based on daner summary stats files... |
| merge_gwascatalog | Merge exac pli constraint data into gene matrix |
| merge_omim | Merge omim phenotypes to gene matrix |
| merge_snpnrs | Merge nr of SNPs per gene used in gene-based test |
| merge_url_links | Merge url links to common resources |
| process_commonmindDLPFC | Process omim morbidmap.txt file (source... |
| process_entrezfile | Preprocess entrez file as downloaded from... |
| process_exacpli | Process exac pli constraint file |
| process_gencodefile | Preprocess gencode file |
| process_gwascatalog | Process exac pli constraint file |
| process_hgncfile | Preprocess hgnc file as downloaded from... |
| process_omim | Process omim morbidmap.txt file (source... |
| publish_genematrix | Save customized gene matrix based on settings |
| uniform_genenames | Standardize gene names to upper case and remove punctuations... |
