Comments (3)
Hi @cantlap,
Thanks for your question. With a quick look, the issue seems likely due to your sample ids in genotype (stored in your annotated GDS file) and phenotype (stored in your null model object) not matching, such that the number of selected samples is always 0. Could you please check on this?
Note that both the annotated GDS file and the null model object are the expected inputs in the STAARpipeline.
Hope this helps.
Best,
Xihao
from staarpipeline-tutorial.
That was the exact issue thank you! It looks like PLINK added a "0_" to the beginning of each ID when making bfiles. I just needed to add the same "0_" to the gds files to match them up.
from staarpipeline-tutorial.
Thank you for confirming, @cantlap. Glad you have resolved this issue, and I shall close this case for now.
Let me know if you have any other questions along the way.
Best,
Xihao
from staarpipeline-tutorial.
Related Issues (20)
- fit_nullmodel Output is mostly Null and 0 HOT 16
- Fitting NULL model for binary outcomes HOT 5
- Error in Gene Centric Analysis HOT 1
- Error in results_plof_genome[, "cMAC"] : subscript out of bounds HOT 2
- Followup Question to Issue #28 HOT 2
- STAARpipeline_Gene_Centric_Noncoding HOT 2
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- [Suggestion-Implementation] Add information to summary and annotations of results HOT 1
- Conditional analysis - Summary Gene Centric Noncoding not running to completion HOT 6
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- Plots for gene centric ncRNA regions HOT 5
- FATAL ERROR - Too many first alleles as the major allele (~21.5%). HOT 1
- warning messages in generating the annotated GDS (aGDS) file. HOT 3
- Controls / cases counts inverted when using binary model HOT 7
- kinship matrix HOT 2
- variant set in gene-centric coding/noncoding analysis HOT 2
- in the Step 2: Individual (single-variant) analysis, Error in if (chr == 1) { : argument is of length zero HOT 3
- Error : Mat::operator(): index out of bounds & Error in apply(emthr_SCANG_O, 2, max) : HOT 1
- What is the difference between the "results_temp" and "results_m" results? HOT 1
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