Hello all, I'm having some trouble understanding the output of the plink association. Any help in the way I'm doing it and in the output would be much appreciated.
So, I got the new Calvin CEL file format and I used the axiom suite to analyze it, exporting them as VCF files. Next based on some forum I did:
VCF files to Plink
./plink --vcf Group.vcf --keep-allele-order --maf 0.05 --allow-extra-chr --make-bed --out test
Generating PED/MAP files
./plink --bfile myplink --recode --allow-extra-chr --out myplinkped
Running PLINK
./plink --file myplinkped --allow-extra-chr
Since these were only people, without any phenotype, we have divided this into 3 groups based on other assays. So I tried to make my own pheno data and running the stats using:
Create your own pheno data then run
../plink --file myplinkped --allow-extra-chr --pheno Pheno.txt --make-bed --allow-no-sex --assoc --out wholeoutput
That's is what my pheno looks like, whereas 1,2,3 in the last column would be the groups I have:
a550995-4396668-081321-759 A01.CEL 0 0 0 1 a550995-4396668-081321-759 A03.CEL 0 0 0 2 a550995-4396668-081321-759 A04.CEL 0 0 0 2 a550995-4396668-081321-759 A05.CEL 0 0 0 2 a550995-4396668-081321-759 B01.CEL 0 0 0 3 a550995-4396668-081321-759 B02.CEL 0 0 0 1 a550995-4396668-081321-759 B03.CEL 0 0 0 2 a550995-4396668-081321-759 B04.CEL 0 0 0 1 a550995-4396668-081321-759 B05.CEL 0 0 0 3 a550995-4396668-081321-759 B12.CEL 0 0 0 3
I got results to make a manhattan plot, however, I do not understand where the p-values are coming from. I had 3 groups and never specified what type of comparison I would like to make. Assuming everything is correct, could you help me understand that?
Thanks in advance
