Standardise summary statistics from GWAS
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Documentation for package ‘MungeSumstats’ version 1.2.1
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| check_ldsc_format | Ensures that parameters are compatible with LDSC format |
| download_vcf | Download VCF file and its index file from Open GWAS |
| find_sumstats | Search Open GWAS for datasets matching criteria |
| format_sumstats | Check that summary statistics from GWAS are in a homogeneous format |
| get_genome_builds | Infer genome builds |
| 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 GWAS |
| index_tabular | Convert summary stats file to tabix format |
| 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 extracted from NCBI dbSNP Build 144. Reference genome version is dependent on user input. |
| raw_ALSvcf | GWAS Amyotrophic lateral sclerosis ieu open GWAS project - Subset |
| raw_eduAttainOkbay | GWAS Educational Attainment Okbay 2016 - Subset |
| read_sumstats | Determine summary statistics file type and read them into memory |
| sumstatsColHeaders | Summary Statistics Column Headers |
| write_sumstats | Write sum stats file to disk |