How to perform classical HLA alleles association analysis

Question

[Angli Xue]

Dear all,

I got an imputed dosage data of classical HLA alleles from software HLA*IMP:02

And I want to run an association analysis of the infectious disease on that.

But I tried with PLINK and didn't see any specific instruction of this kind of analysis.

The HLA data is like

                        HLA_A_101 HLA_A_102 HLA_A_103 HLA_A_201 ....
indvidual 1             0            0           0          0.98
indvidual 2             0            2           0          0
indvidual 3             1            0           0          0
.....
indvidual 1000          0            0           1.99          0

My question is:

1. Can PLINK handle this type of data and run association analysis? If so, how?
2. Any other software can run this kind of analysis?

Cheers,

[Lemire]

I would suggest doing this in R. Check this post and the answer that I gave.