Hi! I'm new about this software and I'm trying to run it out using a SNP data from a custom GWAS in rainbow trout.
I actually have both phenotypes, genotypes, and can create AUC and ROC using the observed and predicted phenotypes (from random animal effect estimated using all the SNP i.e. G-BLUP). However I wanted to give it a try to this software. I have actually two datasets, both genotyped with the same SNP chip.
I have a few questions about this:
1) Is it OK to use all SNP as dominants?
2) I'm running the R script but having a problem once the model ends as follows:
That is the error in spanish. I consulted internet and it says that maybe adding options(expressions = 500000) before the running the script it should work. I did it but the error still appears.
3) Is it completely necessary to include more than one study at the time? Should it work with only one study?
Hi! I'm new about this software and I'm trying to run it out using a SNP data from a custom GWAS in rainbow trout. I actually have both phenotypes, genotypes, and can create AUC and ROC using the observed and predicted phenotypes (from random animal effect estimated using all the SNP i.e. G-BLUP). However I wanted to give it a try to this software. I have actually two datasets, both genotyped with the same SNP chip.
This is my data file
phenotype,dataset,accession,control_size,case_size,risk_allele_freq,OR,model n/a,n/a,1:16977,478,271,0.32973,0.937424742,dominant n/a,n/a,1:33723,478,271,0.475936,0.957853534,dominant n/a,n/a,1:234311,478,271,0.463235,0.980969805,dominant ...
I have a few questions about this: 1) Is it OK to use all SNP as dominants? 2) I'm running the R script but having a problem once the model ends as follows:
[1] "dominant model" [1] "done!!! :)" [1] "-------------------------------------------------------------------" [1] "Analizing study: Datos_IPN_D1" [1] "-------------------------------------------------------------------" Error: protect(): protection stack overflow.
That is the error in spanish. I consulted internet and it says that maybe adding options(expressions = 500000) before the running the script it should work. I did it but the error still appears.
3) Is it completely necessary to include more than one study at the time? Should it work with only one study?
Thats for now, thanks in advance!