Standardise summary statistics from GWAS

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Documentation for package ‘MungeSumstats’ version 1.17.0

• 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