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ERROR: There are no individuals with any non-missing genotypes.

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Contributor
Posts: 57

ERROR: There are no individuals with any non-missing genotypes.

I tried to run the HWE test using following procedure  - And I got the following error

 

ERROR: There are no individuals with any non-missing genotypes.

 

One of the my observation has value Undeter instead of AA or GG etc 

 

How can I fix this issue?

 

proc allele data=SNP393_A outstat=ld prefix=Marker
perms=10000 boot=1000 seed=123 genocol;
var g1-g5;
run;

Super User
Posts: 3,254

Re: ERROR: There are no individuals with any non-missing genotypes.

Posted in reply to mantubiradar19

I'm not familiar with the procedure ALLELE but the error you are getting suggests that your variables g1 to g5 contain only missing values. These variables need to be populated for at least some of your data rows to fix the error.  

Contributor
Posts: 57

Re: ERROR: There are no individuals with any non-missing genotypes.

My variable is a Char type with length of 6 and looks like AA GG CC AT GC etc
Contributor
Posts: 57

Re: ERROR: There are no individuals with any non-missing genotypes.

This is how my dataset looks like! 


Capture.JPG
Super User
Posts: 7,782

Re: ERROR: There are no individuals with any non-missing genotypes.

Posted in reply to mantubiradar19

Read the documentation for the PROC ALLELE statement:

GENOCOL

indicates that columns specified in the VAR statement contain genotypes instead of alleles. When this option is specified, there is one column per marker. The genotypes must consist of the two alleles separated by a delimiter. For a genotype with one missing allele, use a blank space to indicate a missing value; if both alleles are missing, either use a single missing value for the entire genotype or use the delimiter alone.

 

(Bold and underline by me)

 

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Maxims of Maximally Efficient SAS Programmers
Contributor
Posts: 57

Re: ERROR: There are no individuals with any non-missing genotypes.

Posted in reply to KurtBremser
Thanks KurtBremser! I solved it this way

proc allele data=SNP393_A outstat=ld
perms=10000 boot=1000 seed=123 genocol delimiter='';
var g1-g5;
run;
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