check_ldsc_format | Ensures that parameters are compatible with LDSC format |
compute_nsize | Check for N column if not present and user wants, impute N based on user's sample size. *NOTE* this will be the same value for each SNP which is not necessarily correct and may cause issues down the line. N can also be inputted with "ldsc", "sum", "giant" or "metal" by passing one or multiple of these. |
download_vcf | Download VCF file and its index file from Open GWAS |
find_sumstats | Search Open GWAS for datasets matching criteria |
formatted_example | Formatted example |
format_sumstats | Check that summary statistics from GWAS are in a homogeneous format |
get_eff_frq_allele_combns | Get combinations of uncorrected allele and effect (and frq) columns |
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 | Tabix-index file: table |
infer_effect_column | Infer if effect relates to a1 or A2 if ambiguously named |
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 extracted from NCBI dbSNP Build 144. Reference genome version is dependent on user input. |
parse_logs | Parse data from log files |
raw_ALSvcf | GWAS Amyotrophic lateral sclerosis ieu open GWAS project - Subset |
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 memory |
read_vcf | Read in VCF file |
register_cores | Register cores |
standardise_header | Standardise the column headers in the Summary Statistics files |
sumstatsColHeaders | Summary Statistics Column Headers |
vcf2df | VCF to DF |
write_sumstats | Write sum stats file to disk |