Search found 3 matches

by AlfredAlfred
Thu Sep 11, 2014 12:20 pm
Forum: GenABEL
Topic: Variabel pvalues
Replies: 0
Views: 1756

Variabel pvalues

Hi! I am running VariABEL analyses. I want to do Manhattan plots on the pvalues for the variance for each SNP, but I dont know where I should get pvalues from? First I used the "chisq" column, which I had transformed to p-vales (via pchisq). But these pvalues was far to low to be realistic...
by AlfredAlfred
Thu May 22, 2014 1:16 pm
Forum: GenABEL
Topic: Variance GWAS
Replies: 0
Views: 1697

Variance GWAS

Hi

I wonder if it is possible to do variance GWAS on GenABEL?
If not, maybe someone can recommend an R package for this purpose?

Best regards,
A
by AlfredAlfred
Thu May 22, 2014 1:14 pm
Forum: GenABEL
Topic: Duplicate removal
Replies: 1
Views: 1521

Duplicate removal

Hi! I am analyzing Illumina GWAS data. I notice that there are genetic variants that are duplicated, one names rsxxx and one named kgpxxxx. I've been looking for a function in GenAbel to remove these duplicates, but failed. Is there a function for this purpose? Duplicate() didnt work since these SNP...

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