# Standardise summary statistics from GWAS

## Documentation for package ‘MungeSumstats’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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