Base file of PRSice software

shubk · 08-22-2018, 05:25 PM

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

vivek_ · 08-24-2018, 01:13 AM

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.

shubk · 08-24-2018, 02:06 AM

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)}

vivek_ · 08-24-2018, 02:23 AM

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.

shubk · 08-24-2018, 02:56 AM

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

vivek_ · 08-27-2018, 12:57 AM

Beta is the effect size.

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08-22-2018, 05:25 PM	#1
shubk Junior Member Location: India Join Date: Aug 2018 Posts: 5	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

08-24-2018, 01:13 AM	#2
vivek_ PhD Student Location: Denmark Join Date: Jul 2012 Posts: 164	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.

08-24-2018, 02:06 AM	#3
shubk Junior Member Location: India Join Date: Aug 2018 Posts: 5	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)}

08-24-2018, 02:23 AM	#4
vivek_ PhD Student Location: Denmark Join Date: Jul 2012 Posts: 164	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.

08-24-2018, 02:56 AM	#5
shubk Junior Member Location: India Join Date: Aug 2018 Posts: 5	It does have a Beta/OR value for each SNP. Can this value be used instead of effect size?

08-27-2018, 12:57 AM	#6
vivek_ PhD Student Location: Denmark Join Date: Jul 2012 Posts: 164	Beta is the effect size.