Changes in version 6.0.0 - Add new ability to calculate varying prior probabilities based on distance to the gene in eQTL datasets - Add new plot_extended_data function to produce nice QC plots for coloc Changes in version 5.2.3 (2023-10-03) - minor change, for another package to be able to access one of the internal functions, it was exported Changes in version 5.2.2 (2023-05-12) - better checking of dataset inputs, and better documentation of what that data should look like Changes in version 5.2.0 - 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 Changes in version 5.1.2 - deprecate runsusie() argument p Changes in version 5.1.1 - update plot_dataset() and sensitivity() to fix bug for very small p values displaying as 0 Changes in version 5.1.0 (2021-06-14) - release to CRAN of coloc.susie - remove nref now not recommended Changes in version 5.0.0.9002 - in runsusie, allow nref to be overridden if user passes z_ld_weight Changes in version 5.0.0.9001 - 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 Changes in version 4.0-5 - update error checking Changes in version 4.0-3 - BUGFIX - 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) Changes in version 4.0-2 - BUGFIX - 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. Changes in version 4.0-0 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 2019-06-25 Changes in version 3.2-1 (2019-05-17) - 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. Changes in version 3.2 - fix bug in process.datasets which suggested MAF was needed for cc data when beta/varbeta also present - added pkgdown 2018-09-28 Changes in version 3.1 (2018-02-24) 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 2018-02-22 Changes in version 2.4 - added stratification to proportional testing approaches 2017-03-21 Changes in version 2.3-2 - 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 Changes in version 2.3 (2013-09-25) 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. 2013-09-25 Changes in version 2.2 (2013-06-19) - 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. 2013-19-06 Changes in version 2.1 (2013-06-03) - 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. 2013-03-06 Changes in version 2.0 (2013-05-23) - 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. 2013-22-05 Changes in version 1.11 (2013-01-25) - added principal components functions pcs.prepare(), pcs.model(). - Restructed the coloc objects to separate Bayesian and non-Bayesian inference. 2012-12-10 Changes in version 1.10 (2012-11-30) - added Credible Interval calculation to coloc.test(). 2012-11-28 Changes in version 1.09 - updated to return u and Var(u) in addition to chisq statistic. 2012-07-12 Changes in version 1.08 (2012-04-12) - fixed error in documentation, added MASS to Depends. 2012-04-12 Changes in version 1.06 - some tidying. 2012-01-05 Changes in version 1.05 (2012-01-04) - moved to S4 methods. 2012-01-03 Changes in version 1.04 - made the means of generating plots more flexible. 2011-12-27