topic Re: ERROR: There are no individuals with any non-missing genotypes. in SAS Procedures

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

mantubiradar19 — Wed, 25 May 2016 04:01:21 GMT

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;

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

SASKiwi — Wed, 25 May 2016 05:27:22 GMT

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.

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

mantubiradar19 — Wed, 25 May 2016 05:30:33 GMT

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

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

mantubiradar19 — Wed, 25 May 2016 05:31:38 GMT

This is how my dataset looks like!

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

Kurt_Bremser — Wed, 25 May 2016 05:56:18 GMT

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)

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

mantubiradar19 — Wed, 25 May 2016 06:00:43 GMT

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;