Question: Association mapping with plink: what type of phenotypic data?
1
gravatar for beausoleilmo
3.6 years ago by
beausoleilmo320
McGill University
beausoleilmo320 wrote:

I want to know what kind of phenotypic data I can put in PLINK.

I have this phenotypic file (pheno1.txt):

enter image description here

I coded the sex like this: Sex (1=male; 2=female; other=unknown)

Everything is on a continuous scale. no missing values. The IID is the same as the one in the VCF file.

I ran this line:

plink --file output_in_plink --pheno pheno1.txt --out run2

output_in_plink is the files that are named

output_in_plink.ped
output_in_plink.log
output_in_plink.map

Coming from the command vcftools --vcf output.vcf --plink --out ./plink/output_in_plink

After, I ran this:

plink --file output_in_plink --pheno pheno1.txt --out run2

But it returns nothing except a log and a no sex file...

When I ran this:

plink --file output_in_plink --no-fid --pheno pheno1.txt --out run2

It tells me that there si an error:

ERROR: 
Problem with line 1 in [ output_in_plink.ped ]
Expecting 5 + 2 * 840907 = 1681819 columns, but found more

The end goal is to calculate an association mapping of the individuals coming from different populations (4 different species):

plink --file output_in_plink --no-fid --no-parents --pheno pheno1.txt --all-pheno --assoc --maf 0.05 --out run1

But this is not working. Do you know how to solve this?

Maybe I should include the species?:

enter image description here

ADD COMMENTlink modified 3.6 years ago by Fabio Marroni2.6k • written 3.6 years ago by beausoleilmo320
0
gravatar for Fabio Marroni
3.6 years ago by
Fabio Marroni2.6k
Italy
Fabio Marroni2.6k wrote:

From PLINK user manual:

plink --file mydata --pheno pheno.raw --assoc --maf 0.05 --out run1
ADD COMMENTlink written 3.6 years ago by Fabio Marroni2.6k

What's mydata? What's pheno.raw?

ADD REPLYlink written 3.6 years ago by beausoleilmo320

What's mydata? What's pheno.raw?

ADD REPLYlink written 3.6 years ago by beausoleilmo320

mydata=output_in_plink

pheno.raw=pheno1.txt

ADD REPLYlink written 3.6 years ago by Fabio Marroni2.6k

It seems to work but it returns nothing for F_A F_U and CHISQ (from the file run1.assoc).

  1  CHR                    SNP         BP   A1      F_A      F_U   A2        CHISQ   
  2    0            C12915379:2          2    G       NA       NA    T           NA   
  3    0            C12330165:5          5    A       NA       NA    T           NA   
  4    0            C12485604:5          5    A       NA       NA    G           NA   
  5    0            C12707046:5          5    G       NA       NA    C           NA   
  6    0            C13160573:5          5    A       NA       NA    G           NA   
  7    0            C12336575:6          6    T       NA       NA    C           NA

It's saying here that I'm suppose to have a p-value: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml

The weird thing is that they are not proposing a phenotypic file here:

plink --file mydata --assoc
ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by beausoleilmo320
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