Closed pelinunal closed 4 months ago
Hi @pelinunal,
Thank you for your question. This is technically not an error, but rather indicates that your sliding windows do not have a sufficient number of variants to form a valid variant set so that the results will be NULL.
With a quick look, could I ask if your data come from a Whole-Genome Sequencing (WGS) study containing variants from both coding and noncoding regions? Your sample size (11,021) is large, but the number of variants (1.3 million) for this chromosome is relatively small under the sample size being considered, which resulted in NULL
results.
Best, Xihao
Dear @xihaoli,
Indeed, the number of the variants is small in the chr. This is the result of filtering the INFO score >0.9 as a post-QC step after the imputation of the WGS data. Thank you for the enlightment on the problem. I will try with less strict INFO score filtering.
Bests, Pelin
Dear @xihaoli,
In my datasets, I have 11201 samples and there are no errors/problems with performing the other STAARpipeline steps, but only with the
Sliding_Window
step. Eacharrayid
gives the same warnings continuously and eventually the R crushes.I tried to re-install each R package or to change the
sliding_window_length
in various sizes, and the same for the MAF cut-off.A small example from the errors/warnings:
I would like to inform you that there were no significant results from the Dynamic_Window analysis. Is there any possible reason for the NULL outputs and crushes?
Thank you for your time! Bests, Pelin