Colocalisation Tests of Two Genetic Traits

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Documentation for package ‘coloc’ version 5.2.3

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coloc-package Colocalisation tests of two genetic traits
annotate_susie annotate susie_rss output for use with coloc_susie
approx.bf.estimates Internal function, approx.bf.estimates
approx.bf.p Internal function, approx.bf.p
bin2lin binomial to linear regression conversion
check.alignment check alignment
check.dataset check_dataset
check_alignment check alignment
check_dataset check_dataset
coloc.abf Fully Bayesian colocalisation analysis using Bayes Factors
coloc.bf_bf Coloc data through Bayes factors
coloc.detail Bayesian colocalisation analysis with detailed output
coloc.process Post process a coloc.details result using masking
coloc.signals Coloc with multiple signals per trait
coloc.susie run coloc using susie to detect separate signals
coloc.susie_bf run coloc using susie to detect separate signals
coloc_test_data Simulated data to use in testing and vignettes in the coloc package
combine.abf combine.abf
estgeno.1.cse estgeno1
estgeno.1.ctl estgeno1
est_cond generate conditional summary stats
find.best.signal Pick out snp with most extreme Z score
findends trim a dataset to central peak(s)
findpeaks trim a dataset to only peak(s)
finemap.abf Bayesian finemapping analysis
finemap.bf Finemap data through Bayes factors
finemap.signals Finemap multiple signals in a single dataset
logbf_to_pp logbf 2 pp
logdiff logdiff
logsum logsum
map_cond find the next most significant SNP, conditioning on a list of sigsnps
map_mask find the next most significant SNP, masking a list of sigsnps
plot.coloc_abf plot a coloc_abf object
plot_dataset plot a coloc dataset
print.coloc_abf print.coloc_abf
process.dataset process.dataset
runsusie Run susie on a single coloc-structured dataset
sdY.est Estimate trait variance, internal function
sensitivity Prior sensitivity for coloc
subset_dataset subset_dataset
Var.data Var.data
Var.data.cc Var.data