All functions

clump_gwasvcf()

Perform LD clumping

cojo_cond()

Perform conditional analysis using GCTA COJO

cojo_sumstat_file()

Write vcf file to cojo sumstat file

coloc_to_gassocplot()

Convert coloc dataset to gassocplot dataset

gwasvcf_to_TwoSampleMR()

Create exposure or outcome data format for TwoSampleMR from vcf

gwasvcf_to_coloc()

Generate coloc dataset from vcf files

gwasvcf_to_finemapr()

Generate data for fine mapping analysis

harmonise()

Generic harmonisation function

harmonise_against_ref()

Harmonise gwas alleles to be same as reference

ieugwasr_to_TwoSampleMR()

Convert output from query to TwoSampleMR format

ieugwasr_to_coloc()

Generate coloc dataset from the IEU GWAS database

ieugwasr_to_finemapr()

Generate data for analysis in various finemapping methods

ieugwasr_to_gassocplot()

Generate regional plot for ieugwasr

is_forward_strand()

Check a GWAS dataset against a reference known to be on the forward strand

map_variants_to_regions()

For a set of variants map to LD regions

read_gwas()

Read in GWAS dataset

read_reference()

Read in reference dataset

susieR_pipeline()

Perform fine mapping pipeline using susieR

write_out()

Create format for HPC pipeline