coloc 5.1.2

deprecate runsusie() argument p

coloc 5.1.1

update plot_dataset() and sensitivity() to fix bug for very small p values displaying as 0

coloc 5.1.0

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

coloc 5.0.0.9002

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

coloc 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

coloc 4.0-5

update error checking

coloc 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)

coloc 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.

coloc 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

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

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