Package index • genepi.utils

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_gwas(): Harmonise GWAS

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