Convert Binary Plink Files To Human Readable

Question

[marlena.siwiak]

Hi!

I have received three plink files: *bed, *bim, and *fam, from which I need to extract two columns of data in a human readable form. The files contain some information on patients' genotypes and survival times.

I have managed to extract the genotype information by creating a *ped file (under plink 1.07-3 in Debian, Linux):

p-link --bfile mar2 --recode --tab --out outfile

The resulting file contains the following columns (each row is a patient):

family_ID sample_ID paternal_ID maternal_ID sex affection genotype

But there is no information on patients' survival times. Does anybody know how to extract them?

I don't know neither its column name, nor the way this information is encoded in the binaries. Probably I need to list all column names first and guess which one is the right one, but I don't know how to do it. Or maybe there exist some standard way to encode survival times in plink?

I would be grateful for a detailed instruction, as I am not a regular plink user (and don't really want to be - I just need these two columns of data).

Thanks for help.

Answer 1

[zx8754]

PED files:

A PED file must have 1 and only 1 phenotype in the sixth column.

"affection" is your 6th column, which can be either a quantitative trait or an affection status. You might be missing Alternate phenotype files or Covariate files for your data, apart from binary files.

Answer 2

[marlena.siwiak]

In the created ped file I have 7 columns separated by tabs:

idXXX    idXXX     0    0    1    2    T T
idYYY   idYYY    0    0    1    2    C T
...

The nucleotides in the last column are separated by space. I guessed that the sixth column is "affection" based on the manual. Affection or not, it is certainly not the survival time.

You say I'm missing some more files... I cannot exclude that, however, I was assured few times by the research authors that survival times are there - in the binaries. Any ideas how to take them out, or at least check if they are really there?

[Maxime Lamontagne]

In your binaries files, the phenotype is the 6th column of your fam file. If this column is not what you are looking for, then you don't have what you want.