xf-omics
commented
1 year ago Thanks for using our method. We acknowledge that the optimal thresholds may vary between genes. We recommend tailoring the threshold to your dataset. Supplementary Figure S6 illustrates the data distribution and the optimal threshold for our NDD dataset. If uncertain about the best threshold for your data, you can use the default value of 0.
Description
We have been using the SHINE for evaluating the pathogenicity of indels, and find it to be a valuable resource. However, there is an essential piece of information missing: the threshold for evaluating deleteriousness. As of now, neither the GitHub repository nor the associated research article provides any explicit details about the cutoff score used to determine the deleterious nature of indels with the SHINE score.
Proposal
Documentation Update: Request the inclusion of information regarding the threshold, cuttoffs or criteria used to classify indels as deleterious in the official documentation of the SHINE tool.
GitHub Repository Clarification: Suggest adding a section in the README or documentation of the GitHub repository explicitly stating the cutoff score or criteria for evaluating deleteriousness.
Additional Context
The absence of this information makes it challenging for users to set appropriate filters or thresholds for their specific analyses, potentially leading to misinterpretation of results. Clear and concise documentation will enhance the usability of SHINE and promote its accurate application in bioinformatic workflows.
Thank you for your attention to this matter, and I look forward to the clarification on the threshold for evaluating deleteriousness in SHINE.
Best regards