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PRSet Background file #339

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JinhanZhu1 opened this issue Aug 30, 2023 · 4 comments
Closed

PRSet Background file #339

JinhanZhu1 opened this issue Aug 30, 2023 · 4 comments

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@JinhanZhu1
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JinhanZhu1 commented Aug 30, 2023 •
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Hi Sam,

I'm using the PRSet to calculate the competitive-P for gene sets and I have two questions regard to this:

  1. How does PRSet generate construct background SNP set from --background file (Genes)?
    I'm asking this because based on my understanding of this procedures, we have a background SNP set and we constructs null pathways by randomly sampled SNPs from background SNP set, but the required background file we need to input is set of genes. So I wonder if the background SNP set includes all the common SNPs within the range of the genes in the background file or it will only include the SNPs that are in the base file.
  2. The random sample for null pathway generation is with replacement or without replacement selection
    I wonder if the procedure of random sample is with replacement (no repeated selection) or without replacement(one null pathway can have repeated SNPs) from the backend of the algorithm.

Please let me know if my question make sense! I really appreciate your help:)
@choishingwan
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choishingwan commented Aug 30, 2023 via email

@JinhanZhu1
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  1. All snps fall into the gene in the background will be counted (also affect by the wind-3 and wind-5 parameter 2. Without replacement
    …
    On Wed, Aug 30, 2023, 2:20 PM Zhujh @.> wrote: Hi Sam, I'm using the PRSet to calculate the competitive-P for gene sets and I have two questions regard to this: 1. How does PRSet generate construct background SNP set from --background file (Genes)? I'm asking this because based on my understanding of this procedures, we have a background SNP set and we constructs null pathways by randomly sampled SNPs from background SNP set, but the required background file are genes. So I wonder if the background SNP set includes all the common SNPs within the range of the genes in the background file or it will only include the SNPs that are in the base file. 2. The random sample for null pathway generation is with replacement or without replacement selection I wonder if the procedure of random sample is with replacement (no repeated selection) or without replacement(one null pathway can have repeated SNPs) from the backend of the algorithm. Please let me know if my question make sense! I really appreciate your help:) — Reply to this email directly, view it on GitHub <PRSet Background file #339>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYVJJE7HA7FFCD7RLWLXX575BANCNFSM6AAAAAA4E5JARI . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thanks for your reply! The effect size will be based on the base file right? Also, if the without replacement choose the duplicate SNP, the effect size will only be counted once for one null pathway?

@choishingwan
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choishingwan commented Aug 30, 2023 via email

@JinhanZhu1
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ignore my question about duplicated SNPs, I misunderstood without replacement, thanks!

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@choishingwan @JinhanZhu1