Understanding the "OMITTED" column

[Wenbin Mei]

Hi,

The OMITTED column in the hybrid file (output of glm.firth) refers to "Omitted allele" in the documentation. What does that mean? It happens to be similar to the "REF" column. What could have caused this?

Thanks!

Here are the first few columns of my hybrid file:

     CHR     BP          SNP    REF    ALT PROVISIONAL_REF?     A1 OMITTED   A1_FREQ FIRTH?   TEST OBS_CT  
    <num>  <int>       <char> <char> <char>           <char> <char>  <char>     <num> <char> <char>  <int>
 1:     1 766007 1:766007:A:C      A      C                N      C       A 0.0974927      N    ADD  13989
 2:     1 781845 1:781845:A:G      A      G                N      G       A 0.0824642      N    ADD  13989
 3:     1 834056 1:834056:A:C      A      C                N      C       A 0.0297319      N    ADD  13989
 4:     1 838665 1:838665:T:C      T      C                N      C       T 0.0243548      N    ADD  13989
 5:     1 838732 1:838732:G:A      G      A                N      A       G 0.0240304      N    ADD  13989
 6:     1 838890 1:838890:A:G      A      G                N      G       A 0.0242493      N    ADD  13989
 7:     1 838916 1:838916:A:T      A      T                N      T       A 0.0236437      N    ADD  13989
 8:     1 839461 1:839461:T:C      T      C                N      C       T 0.0240903      N    ADD  13989

[Chris Chang]

One allele column has to be omitted from the regression; otherwise the columns are no longer linearly independent (sum of all allele columns is equal to a constant multiple of the intercept column).

https://www.cog-genomics.org/plink/2.0/assoc#omit_ref discusses how the omitted allele is chosen (usually major allele, but you can force REF).

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