R: Colocalisation Tests of Two Genetic Traits

# Colocalisation Tests of Two Genetic Traits

## Documentation for package ‘coloc’ version 5.2.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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