Question: GWAS Make bed file from fam and bim and Polygenic Risk Score calculation
0
gravatar for landscape95
17 months ago by
landscape95170
landscape95170 wrote:

Hi everyone, previously I had a set of bed/bim/fam file in Plink format for GWAS, now I have separate a set of Discovery and Target Samples for Polygenic Risk Score analysis. However, if I select individuals from the .fam file, the bed file will not be suitable for this set of bed/bim/fam file anymore. Does anyone know how to create a new bed file from bim and fam file or am I doing the right way?

Your help is really appreciated!

plink gwas • 760 views
ADD COMMENTlink modified 17 months ago by zx87549.3k • written 17 months ago by landscape95170
1

I don't understand the question. Please clarify. If this is about Plink formats, then:

  • bim is a map file for variants, like chr, pos...
  • fam is a phenotype file, FID, IID, sex, status...
  • bed is a binary genotype file, which is completely useless without having related above bim and fam files.

We cannot create new bed file from bim and fam.

ADD REPLYlink written 17 months ago by zx87549.3k

thank you, that's about Plink format.

ADD REPLYlink written 17 months ago by landscape95170

I have another question, in this case how can I make a Target sample data set, I already had the id of the Discovery and Target set from the total samples which I have in the set of bed/bim/fam file? Thank you very much!

ADD REPLYlink modified 17 months ago • written 17 months ago by landscape95170
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