Known_Loci_Pruning error

[jingling000]

When I execute the script STAARpipelineSummary_Known_Loci_Pruning.r, there are several chromosomes that did not generate corresponding data, and the error is as follows: used (Mb) gc trigger (Mb) max used (Mb) Ncells 283209 15.2 664320 35.5 450929 24.1 Vcells 487090 3.8 8388608 64.0 1815701 13.9 [1] 8

of selected samples: 3,508

of selected variants: 2

of selected samples: 3,508

of selected variants: 2

of selected samples: 3,508

of selected variants: 4,303,007

of selected samples: 3,508

of selected variants: 1

of selected samples: 3,508

of selected variants: 4,303,007

of selected samples: 3,508

of selected variants: 2

Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 没有(非NA)案例可用 Calls: LD_pruning -> Individual_Analysis_cond -> lm -> lm.fit 停止执行 Is the reason for this that the provided known pathogenic loci do not exist in my data? If so, how can I avoid conflicts between removing certain regions during QC and this step?

Thank you for your help.

[xihaoli]

Hi @jingling000,

Thank you for the question. I have been checking what could be the reason that caused this issue, and I recently updated the LD_pruning function, which may be relevant. Could you please install the latest version of the STAARpipeline package and try it again?

Best, Xihao

[jingling000]

Hi Xihao, Thank you very much for your help. I have resolved my issue. Best, Jingling