stephenslab/susieR

Issues

• Multi-allelic SNVs and CNVs

  #237 opened 2 months ago by katherinef
  1

• Set log10bf to max if inf

  #201 opened a year ago by jerome-f
  33

• Expected vs Observed z-scores are not the same

  #236 opened 3 months ago by tamil-acog
  3

• whys the results of fitted_rss1$sets$cs is less than susie_get_cs(fitted_rss1)

  #233 opened 3 months ago by koujiaodahan
  1

• Does the use of "power" in evaluation has frequentist theory grounding?

  #234 opened 3 months ago by garyzhubc
  0

• How to deal with the "." in the vcf file?

  #230 opened 3 months ago by YuhaoDoong
  1

• Can susieR handle large N?

  #220 opened 3 months ago by garyzhubc
  1

• Is it possible to forward sample a specific Susie Model with a / some known causal SNP(s) rather than the posterior?

  #231 opened 3 months ago by garyzhubc
  0

• How to get Fig 3 from Susie (as a frequentist procedure)?

  #232 opened 3 months ago by garyzhubc
  1

• Approximation families

  #235 opened 3 months ago by garyzhubc
  1

• Susie with sparse LD matrices

  #225 opened 6 months ago by nlapier2
  3

• missing value where TRUE/FALSE needed error with susie_rss

  #206 opened a year ago by maguileraf
  18

• Model is not converging evena fter running for 10k iterations

  #226 opened 6 months ago by akhilpampana
  9

• Number of CSs

  #228 opened 6 months ago by Xi-Cao
  5

• susie BLiP

  #229 opened 6 months ago by jerome-f
  1

• Number of CSs

  #227 opened 6 months ago by Xi-Cao
  0

• Confirmation of the sample size value `n`

  #224 opened 6 months ago by laleoarrow
  4

• Also encountered "The estimated prior variance is unreasonably large" using ieugwasr ld_matrix_local function to calculate the ld matrix

  #223 opened 7 months ago by laleoarrow
  20

• `refine` takes long time to run for "small" datasets

  #222 opened 7 months ago by gaow
  3

• Run SuSiE using individual level genetic data

  #221 opened 7 months ago by mkoromina
  4

• SuSiE can crash when run in small samples

  #219 opened 8 months ago by william-denault
  1

• PIP tends to 1 by increasing sample size.

  #218 opened 9 months ago by harryyiheyang
  1

• Behavior of prior_tol and tol thresholds

  #195 opened a year ago by jerome-f
  14

• Feature request summary lbf

  #216 opened 9 months ago by jerome-f
  4

• Is there any rules of thumb on how to set up the prior covariance matrix?

  #215 opened 10 months ago by garyzhubc
  0

• Is it legit to use binary response for susieR?

  #208 opened 10 months ago by garyzhubc
  1

• If I have binary response, is it still possible to use SusieR as a linear probability model instead of a linear regression mode?

  #205 opened 10 months ago by garyzhubc
  1

• How to get regression coefficients from susie?

  #210 opened 10 months ago by garyzhubc
  3

• Is it recommended to partition SNPs into independent regions before fine-mapping or is SuSie Taking care of that?

  #213 opened 10 months ago by garyzhubc
  1

• What is the variational family q_l of equation (3.7)? Is this the only difference from spike-and-slab regression of Carbonetto et al. 2012?

  #214 opened 10 months ago by garyzhubc
  1

• whys lambda is so large

  #212 opened a year ago by koujiaodahan
  2

• kriging_rss plot looks very different despite same processing

  #207 opened a year ago by nickhir
  7

• Does susieR work with very small p-values?

  #211 opened a year ago by vforget
  1

• susie_plot file_prefix doesn't work

  #209 opened a year ago by koujiaodahan
  1

• What pre-processing are required for SusieR? We don't need to remove LD but it looks like we need to centre our data?

  #204 opened a year ago by garyzhubc
  2

• Notion of "inferential statement" in the paper

  #202 opened a year ago by garyzhubc
  8

• Is there any consistency guarantee between CS and joint PIP

  #203 opened a year ago by garyzhubc
  3

• Is it possible to test the hypothesis that the significant variants are in a set of SNPs?

  #196 opened a year ago by garyzhubc
  17

• check_null_threshold

  #197 opened a year ago by jerome-f
  19

• is it acceptable to have pip=1 but posterior beta=0?

  #200 opened a year ago by WeiCSong
  4

• fine-mapping with BOLT-LMM GWAS summary statistics

  #199 opened a year ago by xliaoyi
  3

• Heteroskedasticity?

  #198 opened a year ago by igrabski
  4

• susie_rss lbfs vs susie_ss lbfs

  #194 opened a year ago by zhana-optima
  7

• Genotype-by-environment interaction?

  #193 opened a year ago by Huifang-Xu
  1

• Issue with output cs

  #192 opened a year ago by Huifang-Xu
  10

• res$alpha[i, ] : subscript out of bounds

  #191 opened a year ago by karenfeng
  2

• Correlation matrix is not positive semi-definite

  #190 opened a year ago by karenfeng
  3

• Variant with largest PIP is not included in credible sets

  #189 opened a year ago by VitorAguiar
  15

• Running SusieR with dominance model

  #187 opened a year ago by saulpierotti
  7

• Estimated residual variance is negative

  #188 opened a year ago by karenfeng
  4