coloc 3.2-1

• 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

new function: colocqq - added colocqq for quantitative traits measured on the same individuals - 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

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

• added stratification to proportional testing approaches

2017-03-21

coloc 2.3-2

• 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

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

• 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

• 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

• 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

• 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

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

2012-11-28

coloc 1.09

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

2012-07-12

coloc 1.08

• fixed error in documentation, added MASS to Depends.

2012-04-12

coloc 1.06

• some tidying.

2012-01-05

coloc 1.05

• moved to S4 methods.

2012-01-03

coloc 1.04

• made the means of generating plots more flexible.

2011-12-27