Question: nan in .bim file generated by plink
0
gravatar for dharl
5.8 years ago by
dharl70
India
dharl70 wrote:

Hi all..

I used plink to generate .bed, .bim and .fam files from .ped and .map files. This conversion worked well.

When I access the .bim file, I find nan in the third column in one of the lines of the .bim file, like this: 

1    rs2027305    nan    245672356    A    G

 

This seems to happen after the conversion from .ped and .map file to .bed files. Because of this I am unable to use the .bim file for any analysis and the following error :

 

ERROR: Problem reading BIM file, line 50602

 

Kindly let me know if anyone has encountered this and how this should be handled. 

plink snp • 2.3k views
ADD COMMENTlink modified 5.8 years ago by chrchang5237.1k • written 5.8 years ago by dharl70
3
gravatar for chrchang523
5.8 years ago by
chrchang5237.1k
United States
chrchang5237.1k wrote:

As a temporary measure, you can replace the "nan" with whatever third column value was present on the previous row.  For most purposes, it's also safe to just replace *all* third column values with "0".

ADD COMMENTlink written 5.8 years ago by chrchang5237.1k

Thanks a lot. As of now I have replaced the values of NaNs with a zero. I donot know yet how this will affect the analysis if I do what you have suggested. I will let you know though... 

ADD REPLYlink written 5.8 years ago by dharl70
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