Man pages for richardslab/MRutils
Utility functions for preparing data for Two-Sample MR
| allele_validator | allele information validator |
| assert_chr | Check that input contains a CHR column with values that look... |
| assert_gwas | Validate a dataframe as a gwas |
| assert_probabilities | Check that input is a vector of strings that look like rsids |
| assert_rsids | Check that input contains an rsid column with values that... |
| assert_valid_data | Check that input is a dataframe that validates according to... |
| choose_best_proxies | method to remove ambiguous (palindromic and AF too close to... |
| chr_validator | contig validator |
| demo_data | Snippet of a gwas |
| extract_snps_from_bgzip | Extract a subset of a block-gzipped (and indexed) file by CHR... |
| fill_gwas_unknown_rsids | Method to obtain rsids for records in a gwas where they are... |
| filter_and_write_exposure_data | Method to filter and save exposure data |
| fix_proxy_alleles | Since proxies are provided with a "Correlated_Alleles" column... |
| get_2smr_results | Run Two-Sample MR on pre-processed data. |
| get_cached_rsid_from_position | Get rsid name from position |
| get_LD_pairs | Gets the LD between all the pairs of snps (that are in the... |
| get_proxies | Find proxy snps to the list provided. |
| get_rsid | Get rsid name from position |
| get_rsid_from_position | Get rsid name from position |
| get_unknown_rsids_from_locus | Method to obtain rsids for records in a gwas where they are... |
| gwas_types_validator | gwas column type validator |
| gwas_validator | locus information validator |
| locus_validator | locus information validator |
| merge_rsids_into_gwas | Method to merge back rsids from a subset of a gwas into a... |
| not_in | Not in operator |
| palindromic | List of genotypes that are palindromic |
| pipe | Pipe operator |
| proxy_allele_validator | proxy allele information validator |
| proxy_stats_validator | stats information validator |
| prune_snps | Prunes a collection of SNPs provided in a dataframe. The... |
| remove_linked_snps | Method to select snps so that they are not in LD. |
| replace_alleles | Replaces the alleles in a GWAS according to the replacement... |
| required_headers | List of column headers that are required to be present in a... |
| rsid_validator | rsid information validator |
| stats_validator | stats information validator |
| valid_alleles | List of strings that are valid alleles |
| valid_contigs | List of valid names for a reference sequence/contig in this... |
| valid_contigs_with_chr | List of valid names for a reference sequence/contig in this... |
| valid_references | List of human reference builds that can be used to find rsids |
| vin | vin operator |
