Question: association test using plink
0
gravatar for n_09
5.0 years ago by
n_090
United States
n_090 wrote:

Hi all,

          I have problem with quantitative trait association (plink).I used the following command to run this test: " ./plink --file file_1 --assoc " .I am getting sample.assoc file which is not the output.output file looks something like this:

CHR                SNP         BP   A1      F_A      F_U   A2        CHISQ            P           OR
   1         rs10458597     564621    T    0.012       NA    C           NA           NA           NA
   1         rs12565286     721290    C  0.02846       NA    G           NA           NA           NA
   1         rs12082473     740857    A  0.01181       NA    G           NA           NA           NA

in place of "NA" there should be numerical values which is not in this case.

Thanks in advance

snp • 2.3k views
ADD COMMENTlink modified 5.0 years ago by Lemire590 • written 5.0 years ago by n_090

Could you please paste few lines from your input here?

ADD REPLYlink written 5.0 years ago by cpad011214k

input file test.map looks like this:

1    rs10458597    0    564621
1    rs12565286    0    721290
1    rs12082473    0    740857
1    rs3094315    0    752566
1    rs2286139    0    761732
1    rs2980319    0    777122
1    rs2980300    0    785989
ADD REPLYlink modified 10 months ago by RamRS30k • written 5.0 years ago by n_090

I need few lines from test.map (already provided by you, above) and test.ped (for the snps in example map) so that I can reproduce the error. There are multiple columns with NA. Which column are you expecting to have values?

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by cpad011214k

Thanks. I guess your question is addressed above.

ADD REPLYlink modified 10 months ago by RamRS30k • written 5.0 years ago by cpad011214k
1
gravatar for Lemire
5.0 years ago by
Lemire590
Canada
Lemire590 wrote:

Bases on your output, your command is doing a basic case-control test, where the case/control status is defined in the 6th column of your ped file (taking values 0,1 or 2). In your file, the 6th column probably only contain the value 2, explaining why only F_A contains a non missing value. See this link for case/control tests:

http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#cc

You want to do a quantitative trait, make sure the 6th column contains values other than 0,1,2, or else specify a .phen file. See this link:

http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#qt

ADD COMMENTlink modified 10 months ago by RamRS30k • written 5.0 years ago by Lemire590

Thanks lemire.It worked

ADD REPLYlink written 5.0 years ago by n_090
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