Reference

GWAS standardisation Functions for standardising GWAS inputs
GWAS()	GWAS object
ColumnMap()	ColumnMap object
Column()	Column object
lift()	Liftover GWAS positions
as.data.table()	as.data.table
GWAS processing Functions for prosessing GWAS data
clump()	Clump a GWAS
harmonise()	Harmonise GWAS effects
ld_matrix()	Calculate LD matrix
get_pfile_variants()	Extract variants from plink binary
get_proxies()	Get proxies for variants from plink binary
subset_gwas()	subset_gwas
Mendelian Randomization Functions for performing MR
MR()	MR object
reset_index_snp()	Reset index SNP
clump_mr()	Clump MR object exposure
mr_egger()	Run Egger MR
mr_ivw()	Run IVW MR
mr_pcgmm()	Run PC-GMM MR
mr_results_to_data_table()	MR results to data.table
mr_weighted_median()	Run weighted median MR
mr_weighted_mode()	Run weighted mode MR
run_mr()	Run MR
plot_mr()	Plot MR results
set_ld_mat()	Set the LD matrix
to_MRInput()	Convert to MendelianRandomization::MRInput object
to_MRMVInput()	Convert to MendelianRandomization::MRMVInput object
ld_matrix()	Calculate LD matrix
RSID mapping Functions for mapping chromosome and position data to variant RSIDs
chrpos_to_rsid()	Chromosome & position data to variant RSID
Collider bias Functions for analysing collider / index event bias and adjust GWAS data for this bias.
collider_bias()	Run collider bias assessment
cwls()	Corrected Weighted Least Squares collider bias method
slopehunter()	Slope-Hunter collider bias method
dudbridge()	Dudbridge collider bias method
Plotting Functions for creating common GenEpi data plots
manhattan()	Manhattan plot
miami()	Miami plot
qq_plot()	QQ plot
eaf_plot()	Effect allele frequency plot
generate_random_gwas_data()	Generate random GWAS data
plot_coloc_probabilities()	Coloc probability plot
Setup Functions for package configuration
set_dbsnp_directory()	Set dbSNP directory
which_dbsnp_builds()	Get available dbSNP builds
which_dbsnp_directory()	Get dbSNP directory
set_1000G_reference()	Set the 1000G reference path
set_plink2()	Set the PLINK2 path
which_1000G_reference()	Get 1000G reference path(s)
which_plink2()	Get plink2 path