Question: Information loss in .bgen to .bed conversion
0
gravatar for rbpz
5 months ago by
rbpz0
rbpz0 wrote:

I have a .bgen file of imputed genotyping calls (plus corresponding .sample file), and I have converted the file to .bed format for exploration in R. I converted the file using PLINK --make-bed, read the .bed file into R and ended up with a gene dosage file with 0,1,2, or NAs. In another attempt I tried to convert the .bgen file to .gen and read the .gen file to R. The resulting dosage file is a file with 0,1,2, and non-integer values between 0 and 2 (which I assume are the imputed values).

So my question is: is information lost when converting the files into .bed files? Are imputed non-integer values possible in .bed files? I have read the original .bed file documentation but am still quite confused on this.

Many thanks!

ADD COMMENTlink written 5 months ago by rbpz0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1394 users visited in the last hour