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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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PRSet Background file #339

Closed JinhanZhu1 closed 1 year ago

JinhanZhu1 commented 1 year ago

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 commented 1 year ago

  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 https://github.com/choishingwan/PRSice/issues/339, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYVJJE7HA7FFCD7RLWLXX575BANCNFSM6AAAAAA4E5JARI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

JinhanZhu1 commented 1 year ago
  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 <#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 commented 1 year ago

Yes. Not sure what you meant by duplicated snps

On Wed, Aug 30, 2023, 2:51 PM Zhujh @.***> wrote:

  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 … <#m6893337253488540999> 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 <#339 https://github.com/choishingwan/PRSice/issues/339>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYVJJE7HA7FFCD7RLWLXX575BANCNFSM6AAAAAA4E5JARI 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?

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/339#issuecomment-1699676507, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYS2ZNF5ZXGOEDCTCOTXX6DR3ANCNFSM6AAAAAA4E5JARI . You are receiving this because you commented.Message ID: @.***>

JinhanZhu1 commented 1 year ago

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