Question: SKAT test output explaination
0
gravatar for maroulaki
5.5 years ago by
maroulaki0
United Kingdom
maroulaki0 wrote:

I am running on Plinkseq a SKAT test but I cannot find the output explanation on the documentation.

LOCUS   POS     ALIAS   NVAR    TEST    P       I       DESC

NM_000014       chr12:9220678..9268288  2,A2M   25      SKAT    0.636024        .       1/0(12);1/1(3);10/0(1);2/0(3);3/1(1);3/2(1);3/3(1);6/0(1);6/1(1);9/0(1)

The main question is for the DESC column which is different from simple Burden test

 

Could you pleas help on that?

thanks a lot

next-gen sequence • 1.9k views
ADD COMMENTlink modified 5.1 years ago by vikas1150 • written 5.5 years ago by maroulaki0
0
gravatar for luca.bello
5.5 years ago by
luca.bello30
United States
luca.bello30 wrote:

It seems to be describing the allelic configuration of 25 individuals with rare variants... 12 individuals are heterozygous for variant 1, 3 are homozygous for variant 1, and so forth...

ADD COMMENTlink written 5.5 years ago by luca.bello30
0
gravatar for maroulaki
5.5 years ago by
maroulaki0
United Kingdom
maroulaki0 wrote:

Thanks a lot for the answer

I estimate that 25 refers to NVAR(number of variations) at this area. But I still cannot understand what these genotypes mean 10/0(1);2/0(3);3/1(1);3/2(1);3/3(1);6/0(1);6/1(1);9/0(1) ?

Thanks a lot

ADD COMMENTlink written 5.5 years ago by maroulaki0
0
gravatar for vikas115
5.1 years ago by
vikas1150
vikas1150 wrote:

I would interpret the DESC column to be a summary of the allele counts for the 25 variants used in the burden test: 

1/0(12): 12 variants have 1 carrier in one group and 0 in another 

1/1(3) : 3 variants have 1 carrier each in cases and controls 

10/0: 1 variant has 10 carriers in one group and 0 in another 

and so on. I don't think that the counts are directional (1/0 vs 0/1) but the output for a large number of tests should make this clear. 

 

ADD COMMENTlink written 5.1 years ago by vikas1150
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