stephenslab susieR issues

stephenslab / susieR

R package for "sum of single effects" regression.

https://stephenslab.github.io/susieR

Other

169 stars 41 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

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

#232 garyzhubc opened 1 week ago
1
Is it possible to forward sample a specific Susie Model with a / some known causal SNP(s) rather than the posterior?

#231 garyzhubc opened 1 week ago
0
How to deal with the "." in the vcf file?

#230 YuhaoDoong opened 1 month ago
1
susie BLiP

#229 jerome-f opened 2 months ago
1
Number of CSs

#228 Xi-Cao opened 2 months ago
5
Number of CSs

#227 Xi-Cao closed 2 months ago
0
Model is not converging evena fter running for 10k iterations

#226 akhilpampana opened 2 months ago
9
Susie with sparse LD matrices

#225 nlapier2 opened 2 months ago
3
Confirmation of the sample size value `n`

#224 laleoarrow opened 2 months ago
4
Also encountered "The estimated prior variance is unreasonably large" using ieugwasr ld_matrix_local function to calculate the ld matrix

#223 laleoarrow opened 2 months ago
20
`refine` takes long time to run for "small" datasets

#222 gaow opened 2 months ago
3
Run SuSiE using individual level genetic data

#221 mkoromina closed 3 months ago
4
Can susieR handle large N?

#220 garyzhubc opened 3 months ago
1
SuSiE can crash when run in small samples

#219 william-denault opened 4 months ago
1
PIP tends to 1 by increasing sample size.

#218 harryyiheyang opened 4 months ago
1
Speed up estimate_s_rss

#217 aksarkar closed 5 months ago
4
Feature request summary lbf

#216 jerome-f opened 5 months ago
4
Is there any rules of thumb on how to set up the prior covariance matrix?

#215 garyzhubc opened 6 months ago
0
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 garyzhubc closed 6 months ago
1
Is it recommended to partition SNPs into independent regions before fine-mapping or is SuSie Taking care of that?

#213 garyzhubc closed 6 months ago
1
whys lambda is so large

#212 koujiaodahan opened 6 months ago
2
Does susieR work with very small p-values?

#211 vforget opened 6 months ago
1
How to get regression coefficients from susie?

#210 garyzhubc closed 6 months ago
3
susie_plot file_prefix doesn't work

#209 koujiaodahan opened 6 months ago
1
Is it legit to use binary response for susieR?

#208 garyzhubc closed 6 months ago
1
kriging_rss plot looks very different despite same processing

#207 nickhir opened 7 months ago
7
missing value where TRUE/FALSE needed error with susie_rss

#206 maguileraf opened 7 months ago
18
If I have binary response, is it still possible to use SusieR as a linear probability model instead of a linear regression mode?

#205 garyzhubc closed 6 months ago
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 garyzhubc opened 8 months ago
2
Is there any consistency guarantee between CS and joint PIP

#203 garyzhubc opened 8 months ago
3
Notion of "inferential statement" in the paper

#202 garyzhubc opened 8 months ago
8
Set log10bf to max if inf

#201 jerome-f opened 8 months ago
3
is it acceptable to have pip=1 but posterior beta=0?

#200 WeiCSong opened 9 months ago
4
fine-mapping with BOLT-LMM GWAS summary statistics

#199 xliaoyi closed 9 months ago
3
Heteroskedasticity?

#198 igrabski opened 10 months ago
4
check_null_threshold

#197 jerome-f closed 9 months ago
19
Is it possible to test the hypothesis that the significant variants are in a set of SNPs?

#196 garyzhubc opened 11 months ago
17
Behavior of prior_tol and tol thresholds

#195 jerome-f opened 1 year ago
14
susie_rss lbfs vs susie_ss lbfs

#194 zhana-optima opened 1 year ago
7
Genotype-by-environment interaction?

#193 Huifang-Xu opened 1 year ago
1
Issue with output cs

#192 Huifang-Xu opened 1 year ago
10
res$alpha[i, ] : subscript out of bounds

#191 karenfeng opened 1 year ago
2
Correlation matrix is not positive semi-definite

#190 karenfeng opened 1 year ago
3
Variant with largest PIP is not included in credible sets

#189 VitorAguiar closed 1 year ago
15
Estimated residual variance is negative

#188 karenfeng opened 1 year ago
4
Running SusieR with dominance model

#187 saulpierotti opened 1 year ago
7
fine-mapping using susieR with summary statistics from QTLtools or with individual genotype data?

#186 caydenpenn opened 1 year ago
10
Tolerate NaNs in susie_rss shat

#185 karenfeng opened 1 year ago
1
run susie_rss for MHC region

#184 PhoebeGuo97 opened 1 year ago
4
Repo License?

#183 carlaost closed 1 year ago
2