| api_query | Wrapper for sending queries and payloads to API |
| axel | axel downloader |
| check_access_token | Check if authentication has been made |
| check_allele_flip | Ensure A1 & A2 are correctly named, if GWAS SNP constructed... |
| check_allele_merge | Ensure that A1:A2 or A1/A2 or A1>A2 or A2>A1 aren't merged... |
| check_bi_allelic | Remove non-biallelic SNPs |
| check_bp_range | Ensure that the Base-pair column values are all within the... |
| check_chr | Standardize the CHR column |
| check_col_order | Ensure that the first three columns are SNP, CHR, BP in that... |
| check_drop_indels | Drop Indels from summary statistics |
| check_dup_bp | Ensure all rows have unique positions, drop those that don't |
| check_dup_col | Ensure that no columns are duplicated |
| check_dup_row | Ensure all rows are unique based on SNP,CHR,BP,A1,A2, drop... |
| check_dup_snp | Ensure all rows have unique SNP IDs, drop those that don't |
| check_effect_columns_nonzero | Ensure that the standard error (se) is positive for all SNPs |
| check_empty_cols | Check for empty columns |
| check_four_step_col | Ensure that CHR:BP:A2:A1 aren't merged into 1 column |
| check_frq | Ensure all SNPs have frq score above threshold |
| check_frq_maf | Check that FRQ column refers to minor/effect allele frequency... |
| check_info_score | Ensure all SNPs have info score above threshold |
| check_ldsc_format | Ensures that parameters are compatible with LDSC format |
| check_miss_data | Remove SNPs with missing data |
| check_multi_gwas | Ensure that only one model in GWAS sumstats or only one trait... |
| check_multi_rs_snp | Ensure that SNP ids don't have multiple rs ids on one line |
| check_n_int | Ensure that the N column is all integers |
| check_n_num | Ensure all SNPs have N less than X std dev below mean |
| check_no_allele | Ensure that A1 & A2 are present, if not can find it with SNP... |
| check_no_chr_bp | Ensure that CHR and BP are missing if SNP is present, can... |
| check_no_rs_snp | Ensure that SNP appears to be valid RSIDs (starts with rs) |
| check_no_snp | Ensure that SNP is present if not can find it with CHR and BP |
| check_numeric | Check numeric columns |
| check_on_ref_genome | Ensure all SNPs are on the reference genome |
| check_pos_se | Ensure that the standard error (se) is positive for all SNPs... |
| check_range_p_val | Ensure that the p values are not >1 and if so set to 1 |
| check_row_snp | Ensure all rows have SNPs beginning with rs or SNP, drop... |
| check_save_path | Check if save path and log folder is appropriate |
| check_signed_col | Ensure that there is at least one signed column in summary... |
| check_small_p_val | Ensure that the non-negative p-values are not 5e-324 or... |
| check_strand_ambiguous | Remove SNPs with strand-ambiguous alleles |
| check_tabular | Ensure valid tabular format |
| check_two_step_col | Ensure that CHR:BP aren't merged into 1 column |
| check_vcf | Check if the inputted file is in VCF format |
| check_vital_col | Ensure that all necessary columns are in the summary... |
| check_zscore | Check for Z-score column |
| column_dictionary | Map column names to positions. |
| compute_nsize | Check for N column if not present and user wants, impute N... |
| compute_sample_size | Compute (effective) sample size |
| compute_sample_size_n | Add user supplied sample size |
| compute_sample_size_neff | Compute Neff/N |
| convert_sumstats | Convert summary statistics to desired object type |
| DF_to_dt | DataFrame to data.table |
| downloader | downloader wrapper |
| download_vcf | Download VCF file and its index file from Open GWAS |
| drop_duplicate_cols | Drop duplicate columns |
| drop_duplicate_rows | Drop duplicate rows |
| find_sumstats | Search Open GWAS for datasets matching criteria |
| format_sumstats | Check that summary statistics from GWAS are in a homogeneous... |
| formatted_example | Formatted example |
| get_access_token | Get access token for OAuth2 access to MR Base |
| get_chain_file | Download chain file for liftover |
| get_eff_frq_allele_combns | Get combinations of uncorrected allele and effect (and frq)... |
| get_genome_build | Infers the genome build of the summary statistics file... |
| get_genome_builds | Infer genome builds |
| get_query_content | Parse out json response from httr object |
| get_unique_name_log_file | Simple function to ensure the new entry name to a list... |
| get_vcf_sample_ids | Get VCF sample ID(s) |
| granges_to_dt | GenomicRanges to data.table |
| gwasinfo | Get list of studies with available GWAS summary statistics... |
| hg19ToHg38 | UCSC Chain file hg19 to hg38 |
| hg38ToHg19 | UCSC Chain file hg38 to hg19 |
| ieu-a-298 | Local ieu-a-298 file from IEU Open GWAS |
| import_sumstats | Import full genome-wide GWAS summary statistics from Open... |
| index_tabular | Tabix-index file: table |
| index_vcf | Tabix-index file: VCF |
| infer_effect_column | Infer if effect relates to a1 or A2 if ambiguously named |
| is_tabix | Is tabix |
| legacy_ids | Convert current IDs to legacy IDs |
| liftover | Genome build liftover |
| list_sumstats | List munged summary statistics |
| load_ref_genome_data | Load the reference genome data for SNPs of interest |
| load_snp_loc_data | Loads the SNP locations and alleles for Homo sapiens... |
| logs_example | Example logs file |
| make_allele_upper | Ensure A1 and A2 are upper case |
| message_parallel | Send messages to console even from within parallel processes |
| messager | Print messages |
| parse_dropped_chrom | Parse number of SNPs dropped due to being on chrom X, Y or MT |
| parse_dropped_duplicates | Parse number of SNPs dropped due to being duplicates |
| parse_dropped_INFO | Parse number of SNPs dropped due to being below the INFO... |
| parse_dropped_nonA1A2 | Parse number of SNPs dropped due to not matching the ref... |
| parse_dropped_nonBiallelic | Parse number of SNPs dropped due to not being bi-allelic |
| parse_dropped_nonRef | Parse number of SNPs dropped due to being in the ref genome |
| parse_flipped | Parse number of SNPs flipped to align with the ref genome |
| parse_genome_build | Genome build inferred from the summary statistics |
| parse_idStandard | Standardised IEU MRC OpenGWAS ID |
| parse_logs | Parse data from log files |
| parse_pval_large | Parse number of SNPs with p-values >1 |
| parse_pval_neg | Parse number of SNPs with p-values <0 |
| parse_pval_small | Parse number of SNPs with non-negative p-values <=5e-324 |
| parse_report | Parse "Summary statistics report" metrics |
| parse_snps_freq_05 | Parse number/percent of SNPs with FREQ values >0.5 |
| parse_snps_not_formatted | Parse number of SNPs not correctly formatted |
| parse_time | Parse the total time taken the munge the file |
| preview_sumstats | Preview formatted sum stats saved to disk |
| raw_ALSvcf | GWAS Amyotrophic lateral sclerosis ieu open GWAS project -... |
| raw_eduAttainOkbay | GWAS Educational Attainment Okbay 2016 - Subset |
| read_header | Read in file header |
| read_sumstats | Determine summary statistics file type and read them into... |
| read_vcf | Read in VCF file |
| read_vcf_genome | Read VCF genome |
| read_vcf_info | Read VCF: INFO column |
| read_vcf_markername | Read VCF: MarkerName column |
| read_vcf_parallel | Read VCF: parallel |
| read_vcf_pval | Read VCF: p-value column |
| register_cores | Register cores |
| remove_empty_cols | Remove empty columns |
| report_summary | Report info on current state of the summary statistics |
| select_api | Toggle API address between development and release |
| select_vcf_fields | Select VCF fields |
| sort_coord_genomicranges | Sort sum stats: GenomicRanges |
| sort_coords | Sort sum stats |
| sort_coords_datatable | Sort sum stats: data.table |
| standardise_header | Standardise the column headers in the Summary Statistics... |
| sumstatsColHeaders | Summary Statistics Column Headers |
| supported_suffixes | List supported file formats |
| to_granges | To 'GRanges' |
| to_vranges | Convert to 'VRanges' |
| unlist_dt | Unlist a data.table |
| validate_parameters | Ensure that the input parameters are logical |
| vcf2df | VCF to DF |
| write_sumstats | Write sum stats file to disk |
