• better checking of dataset inputs, and better documentation of what that data should look like
  • update to new susieR >= 0.12.06 which requires sample size
  • general tidy up of susie-related code
  • new functions to help find subregions for finemapping - findpeaks, findends
  • updated FAQ.md
  • tidied empty items in documentation to make CRAN happy
  • slimmed down example dataset to make CRAN even happier
  • deprecate runsusie() argument p
  • update plot_dataset() and sensitivity() to fix bug for very small p values displaying as 0
  • release to CRAN of coloc.susie
  • remove nref now not recommended
  • in runsusie, allow nref to be overridden if user passes z_ld_weight
  • deprecate coloc.signals for multiple causal variants
  • introduce coloc.susie for multiple causal variants
  • new vignette 02_data giving more details on structuring your data properly
  • update error checking
  • missing sdY for type=“quant” would error in finemap.signals or coloc.signals, now it is estimated if missing.
  • warning for factors used as snp names added (issue #29)
  • snps in the second dataset might not have been masked as intended. This would result in effect using the “single” option for trait 2 when masking was expected.

new functions: coloc.signals, finemap.abf - analogues of coloc.abf and finemap.abf that allow for multiple causal variants. See vignette on conditioning/masking new function: sensitivity - post-hoc, determine the sensitivity of coloc results to changes in the prior. See vignette on sensitivity


  • BUGFIX: finemap.abf()
  • in low power situations, the posterior for H0 was previously too low. This will only affect datasets where the minimum p value was > 1e-7 - ie where the posterior for H0 would be expected to be much above 0.
  • fix bug in process.datasets which suggested MAF was needed for cc data when beta/varbeta also present
  • added pkgdown


new function: finemap.abf - improved clarity of error messages in coloc.abf() sub functions - added finemap.abf to fine map a single trait - fixed warnings caused by CRAN disliking the BioConductor devel branch


  • added stratification to proportional testing approaches


  • tidied code relating mainly to proportional
  • colocalisation testing methods, making more methods confirm to S4.
  • pcs.prepare now imputes missing genotypes by default 2013-05-22

coloc BUGFIX

  • Introduced a function to estimate trait variance from supplied coefficients and standard errors. This is used within the approach implemented in coloc.abf(), and replaces the earlier version which implicitly assumed that var(Y)=1 for quantitative traits, which could lead to incorrect inference when var(Y) was far from 1.


  • Merged coloc.abf and coloc.abf.imputed(), so that datasets for which beta, var(beta) are available can be matched to datasets with only p values and maf.2 This means the arguments to coloc.abf() have been changed! Please check ?coloc.abf for the new function.


  • Bug fix for coloc.abf() function, which used p12 instead of log(p12) to calculate L4.
  • New function coloc.abf.imputed() to make better use of fuller information on imputed data.


  • New function, coloc.abf(), to implement the colocalisation approach described by Giambartolomei et. al.
  • Changes in the coloc.test() and coloc.bma() functions to make them consistent with regards arguments and output.


  • added principal components functions pcs.prepare(), pcs.model().
  • Restructed the coloc objects to separate Bayesian and non-Bayesian inference.


  • added Credible Interval calculation to coloc.test().


  • updated to return u and Var(u) in addition to chisq statistic.


  • fixed error in documentation, added MASS to Depends.


  • some tidying.


  • moved to S4 methods.


  • made the means of generating plots more flexible.