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PRSet Background file #339
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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:)
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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? |
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
… <#m_6893337253488540999_>
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
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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?
—
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ignore my question about duplicated SNPs, I misunderstood without replacement, thanks! |
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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:
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.
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:)
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