coloc 5.1.0 Unreleased

  • release to CRAN of coloc.susie
  • remove nref now not recommended

coloc 5.0.0.9002 Unreleased

  • in runsusie, allow nref to be overridden if user passes z_ld_weight

coloc 5.0.0.9001 Unreleased

  • 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

coloc 4.0-5 Unreleased

  • update error checking

coloc 4.0-3 Unreleased

  • 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)

coloc 4.0-2 Unreleased

  • 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.

coloc 4.0-0 Unreleased

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

coloc 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.

coloc 3.2 Unreleased

  • fix bug in process.datasets which suggested MAF was needed for cc data when beta/varbeta also present
  • added pkgdown

2018-09-28

coloc 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

coloc 2.4 Unreleased

  • added stratification to proportional testing approaches

2017-03-21

coloc 2.3-2 Unreleased

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

coloc 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 implicity assumed that var(Y)=1 for quantitative traits, which could lead to incorrect inference when var(Y) was far from 1.

2013-09-25

coloc 2.2 2013-06-19

  • Merged coloc.abf and coloc.abf.imputed(), so that datasets for wheich 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

coloc 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

coloc 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

coloc 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

coloc 1.10 2012-11-30

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

2012-11-28

coloc 1.09 Unreleased

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

2012-07-12

coloc 1.08 2012-04-12

  • fixed error in documentation, added MASS to Depends.

2012-04-12

coloc 1.06 Unreleased

  • some tidying.

2012-01-05

coloc 1.05 2012-01-04

  • moved to S4 methods.

2012-01-03

coloc 1.04 Unreleased

  • made the means of generating plots more flexible.

2011-12-27