Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Base file of PRSice software

    I am using PRSice software for Polygenic risk score calculation of complex diseases like Type 2 Diabetes, Coronary artery disease. Input files required for analysis are Base file (example: TOY_BASE_GWAS.assoc ) and target file (binary files from plink for your target data). I am able to create target files using plink plug in from genome studio .,but Don't know how to create gwas association file for my phenotype like Type 2 Diabetes

  • #2
    You'll have to search the highest powered GWAS of T2D and download the association results. That's the base file on which you are going to build the predictive model.

    Comment


    • #3
      Thank you. I have downloaded association results from GWAS. The file has all required columns except effect size estimates, is there is any way to calculate it ? or is PRSice can run without effect size info in base file.
      {PRSice requires the base file to contain information of the effective allele (--A1), effect size estimates (--stat)}

      Comment


      • #4
        Does it not have a Beta? If you have a z-score and p-value you can compute a beta from them using inverse probability transformation. You can read up on this online and get a formula to do so.

        Comment


        • #5
          It does have a Beta/OR value for each SNP. Can this value be used instead of effect size?

          Comment


          • #6
            Beta is the effect size.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Best Practices for Single-Cell Sequencing Analysis
              by seqadmin



              While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
              06-06-2024, 07:15 AM
            • seqadmin
              Latest Developments in Precision Medicine
              by seqadmin



              Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

              Somatic Genomics
              “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
              05-24-2024, 01:16 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 06-21-2024, 07:49 AM
            0 responses
            14 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 06-20-2024, 07:23 AM
            0 responses
            14 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 06-17-2024, 06:54 AM
            0 responses
            16 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 06-14-2024, 07:24 AM
            0 responses
            25 views
            0 likes
            Last Post seqadmin  
            Working...
            X