error when running coloc.SuSie

[schavezchavez]

Dear chris,

Thanks a lot for the new SuSie colocalization tool! I have been trying to get it running to perform colocalization analysis. I got my data sets checked by the check.dataset function, and they were found correct (NULL exit). I then tried to run coloc.susie but i keep getting the error below. This error results in an empty results object. running iterations: 100 converged: TRUE running iterations: 100 converged: TRUE Warning messages: 1: In (function (z, R, maf = NULL, maf_thresh = 0, z_ld_weight = 0, : The z_ld_weight > 0 feature is under development. 2: In (function (z, R, maf = NULL, maf_thresh = 0, z_ld_weight = 0, : The z_ld_weight > 0 feature is under development.

i was wondering if you know how to troubleshoot this.

Thanks in advance,

[chr1swallace]

Hi Sergio, that's a warning not am error.

What's the output of using runsusie() on each of your datasets?

C

⁣http://chr1swallace.github.io​

On 3 Apr 2021, 19:56, at 19:56, Sergio Chavez @.***> wrote:

Dear chris,

Thanks a lot for the new SuSie colocalization tool! I have been trying to get it running to perform colocalization analysis. I got my data sets checked by the check.dataset function, and they were found correct (NULL exit). I then tried to run coloc.susie but i keep getting the error below. This error results in an empty results object. running iterations: 100 converged: TRUE running iterations: 100 converged: TRUE Warning messages: 1: In (function (z, R, maf = NULL, maf_thresh = 0, z_ld_weight = 0, : The z_ld_weight > 0 feature is under development. 2: In (function (z, R, maf = NULL, maf_thresh = 0, z_ld_weight = 0, : The z_ld_weight > 0 feature is under development.

i was wondering if you know how to troubleshoot this.

Thanks in advance,

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[schavezchavez]

Hi Chris, when running runsusie i get the same warning. i see for one dataset (qtl data - S3) i get some results, but for my gwas dataset (S4) i don't get any output. see below

summary(S3) Variables in credible sets: variable variable_prob cs 34 1.0000000 2 29 0.9640969 1 35 0.6013686 1 39 0.6013686 1 38 0.5438996 1 Credible sets summary: cs cs_log10bf cs_avg_r2 cs_min_r2 variable 2 115.51769 1.0000000 1.0000000 34 1 85.59643 0.9999991 0.9999973 29,35,38,39 summary(S4) Variables in credible sets: [1] variable variable_prob cs

<0 rows> (or 0-length row.names) Credible sets summary: data frame with 0 columns and 0 rows

[chr1swallace]

It seems Susie doesn't find any credible sets. What do your p values look like for that dataset, is there a signal to be found?

⁣http://chr1swallace.github.io​

On 6 Apr 2021, 08:19, at 08:19, Sergio Chavez @.***> wrote:

Hi Chris, when running runsusie i get the same warning. i see for one dataset (qtl data - S3) i get some results, but for my gwas dataset (S4) i don't get any output. see below

summary(S3) Variables in credible sets: variable variable_prob cs 34 1.0000000 2 29 0.9640969 1 35 0.6013686 1 39 0.6013686 1 38 0.5438996 1 Credible sets summary: cs cs_log10bf cs_avg_r2 cs_min_r2 variable 2 115.51769 1.0000000 1.0000000 34 1 85.59643 0.9999991 0.9999973 29,35,38,39 summary(S4) Variables in credible sets: [1] variable variable_prob cs

<0 rows> (or 0-length row.names) Credible sets summary: data frame with 0 columns and 0 rows

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[schavezchavez]

Yeah. i am not completely familiar with this kind of analyses. In mijn Gwas dataset i have all the snps from one locus and they all have genome wide significant p values, as well as being all in very high LD and having more or less the same beta. I have in my qtl dataset 40ish snps and in my gwas i have 160 snps. all the 40 snps from the qtl dataset overlap with gwas dataset btw. do you think i am lacking power to do this kind of analysis? or something else influencing it?

[chr1swallace]

Then may I suggest you start here https://chr1swallace.github.io/coloc/articles/a02_data.html with some description of how to prepare data for coloc?

On Tue, 2021-04-06 at 00:32 -0700, Sergio Chavez wrote:

Yeah. i am not completely familiar with this kind of analyses. In mijn Gwas dataset i have all the snps from one locus and they all have genome wide significant p values, as well as being all in very high LD and having more or less the same beta. I have in my qtl dataset 40ish snps and in my gwas i have 160 snps. all the 40 snps from the qtl dataset overlap with gwas dataset btw. do you think i am lacking power to do this kind of analysis? or something else influencing it?

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[schavezchavez]

Oke. thank you very much Chris. I will check it out.