Coloc v2.2 is up on CRAN. The last two changes are shown below. The important thing is that the arguments to
coloc.abf() have changed. Please do revise your code!
I do try and avoid completely changing arguments to released functions, but in this case, the function was introduced relatively recently, and the change makes sense because it allows us to analyse either datasets for which coefficients and standard errors are available, or for which only p values and minor allele frequencies are available, in a single function.
2013-19-06 Chris Wallace <email@example.com> * v2.2 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.
2013-03-06 Chris Wallace <firstname.lastname@example.org> * v2.1 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.