Function reference • MungeSumstats

All functions
`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
`format_sumstats()`	Check that summary statistics from GWAS are in a homogeneous format
`formatted_example()`	Formatted example
`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
`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

Reference

All functions