pcarbo/varbvs issues and pull requests

#44 - Is it recommended to standardize data matrix X before feeding into varbvs?

Issue - State: open - Opened by garyzhubc 6 months ago

#43 - Is it better to use PIP or Bayes factor for variable selection?

Issue - State: open - Opened by garyzhubc 7 months ago - 3 comments

#42 - Scale invariance

Issue - State: open - Opened by nlapier2 about 1 year ago - 3 comments

#41 - Does the size of the PIP matters? Is it worth reporting if I get a bunch of small PIP values? 0.02 or so.

Issue - State: open - Opened by garyzhubc about 1 year ago

#40 - How to plot PIP in log scale?

Issue - State: open - Opened by garyzhubc about 1 year ago

#39 - Shall I put the entire chromosome in varbvs given that it's computationally feasible to do so?

Issue - State: open - Opened by garyzhubc about 1 year ago

#38 - How to set success rate \pi?

Issue - State: closed - Opened by garyzhubc about 1 year ago - 1 comment

#37 - trouble plotting

Issue - State: closed - Opened by garyzhubc about 1 year ago - 1 comment

#36 - Inconsistencies between simulated and calculated pip

Issue - State: closed - Opened by garyzhubc about 1 year ago

#35 - How to sample from the posterior?

Issue - State: open - Opened by garyzhubc over 1 year ago - 2 comments

#34 - Do you recommend pruning SNPs that are in linkage disequilibrium before putting into varbvs?

Issue - State: open - Opened by garyzhubc almost 4 years ago - 3 comments

#33 - Do you recommend including principal components as covariates to control for population stratification?

Issue - State: closed - Opened by garyzhubc almost 4 years ago - 1 comment

#32 - How to tune the model when it shows a lot of small probabilities around a region known to be highly relevant to the phenotype?

Issue - State: closed - Opened by garyzhubc almost 4 years ago - 1 comment

#31 - Is this an indication of the non-convergence of the algorithm?

Issue - State: closed - Opened by garyzhubc almost 4 years ago - 5 comments

#30 - Why varbvs doesn't accept datasets with missing genotype?

Issue - State: closed - Opened by garyzhubc almost 4 years ago - 1 comment

#29 - Can you support .bed or .bgen files?

Issue - State: closed - Opened by garyzhubc almost 4 years ago - 9 comments

#28 - Parallel execution of loop over grid of "logodds"

Issue - State: open - Opened by fmorgante over 4 years ago

#27 - Undefined function or variable 'fit'

Issue - State: closed - Opened by xiangzhu over 6 years ago - 1 comment

#26 - Log-odds based on 10

Issue - State: closed - Opened by xiangzhu over 6 years ago - 2 comments

#25 - Mex flag `-DMATLAB_MEX_FILE`

Issue - State: closed - Opened by xiangzhu over 6 years ago - 6 comments

#24 - show inference for pi in print.summary.varbvs

Issue - State: open - Opened by timflutre over 6 years ago - 4 comments
Labels: enhancement, documentation

#23 - keep same output for confint whether one or several variables are given

Issue - State: closed - Opened by timflutre over 6 years ago - 6 comments

#22 - list top variables based on their PIP

Issue - State: closed - Opened by timflutre over 6 years ago - 2 comments

#21 - question on assigning prior logodds to input data

Issue - State: closed - Opened by YSanchezAraujo over 6 years ago - 2 comments

#20 - Z values- categorical covariates with multiple levels

Issue - State: open - Opened by RohitThakur01 almost 7 years ago - 1 comment
Labels: documentation

#19 - Random Effect

Issue - State: open - Opened by camult about 7 years ago - 1 comment

#18 - allow to pass weights to varbvs()

Issue - State: open - Opened by timflutre about 7 years ago - 13 comments
Labels: enhancement

#17 - Add "update.order" argument to varbvs function

Issue - State: closed - Opened by pcarbo over 7 years ago - 1 comment
Labels: enhancement

#16 - problems when X is not double precision

Issue - State: closed - Opened by stephens999 over 7 years ago - 6 comments

#15 - An edge case with `varbvsmix`

Issue - State: closed - Opened by gaow over 7 years ago - 2 comments
Labels: bug, documentation

#14 - subroutine missing

Issue - State: closed - Opened by xiangzhu over 7 years ago - 4 comments

#13 - Rcpp implementation for varbvsnormupdate.

Pull Request - State: closed - Opened by dcgerard about 8 years ago - 1 comment

#12 - get problem of mexing the c file

Issue - State: open - Opened by bruce803 over 8 years ago - 3 comments

#11 - Update mvash branch.

Pull Request - State: closed - Opened by pcarbo over 8 years ago

#10 - The two-stage fitting procedure is not available when ns == 1

Issue - State: closed - Opened by xiangzhu almost 9 years ago - 1 comment

#9 - Definitions of sa are different between varbvs 1.0 and 2.0

Issue - State: closed - Opened by xiangzhu almost 9 years ago - 5 comments

#8 - Inf is not allowed for options.maxiter

Issue - State: closed - Opened by xiangzhu almost 9 years ago - 1 comment

#7 - broken paper link in readme

Issue - State: closed - Opened by xiangzhu almost 9 years ago - 1 comment