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clump_gwasvcf()
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Perform LD clumping |
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cojo_cond()
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Perform conditional analysis using GCTA COJO |
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cojo_sumstat_file()
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Write vcf file to cojo sumstat file |
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coloc_to_gassocplot()
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Convert coloc dataset to gassocplot dataset |
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gwasvcf_to_TwoSampleMR()
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Create exposure or outcome data format for TwoSampleMR from vcf |
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gwasvcf_to_coloc()
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Generate coloc dataset from vcf files |
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gwasvcf_to_finemapr()
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Generate data for fine mapping analysis |
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harmonise()
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Generic harmonisation function |
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harmonise_against_ref()
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Harmonise gwas alleles to be same as reference |
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ieugwasr_to_TwoSampleMR()
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Convert output from query to TwoSampleMR format |
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ieugwasr_to_coloc()
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Generate coloc dataset from the IEU GWAS database |
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ieugwasr_to_finemapr()
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Generate data for analysis in various finemapping methods |
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ieugwasr_to_gassocplot()
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Generate regional plot for ieugwasr |
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is_forward_strand()
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Check a GWAS dataset against a reference known to be on the forward strand |
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make_TwoSampleMR_dat()
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Create a harmonised dataset from lists of vcf files |
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map_variants_to_regions()
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For a set of variants map to LD regions |
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organise_ids()
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Figure out specific files and IDs depending on what files exist and whethet vcfdir is set |
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read_gwas()
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Read in GWAS dataset |
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read_reference()
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Read in reference dataset |
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set_bc4_files()
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Determine locations of useful reference datasets on bluecrystal4 |
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susieR_pipeline()
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Perform fine mapping pipeline using susieR |
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write_out()
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Create format for HPC pipeline |