Plink allele scoring output

Question

[NB]

Hello,

I am using PLINK2 to create a profile score and am confused to what the output represent:

My score file has ~84k SNPs and my profile output looks like this

 FID  IID  PHENO    CNT   CNT2    SCORE
  00    1      1 173748  83462 0.017818
  01    1      1 173740  83216 0.017095
  02    2      1 173728  83738 0.017375

Plink says

CNT  -Number of non-missing SNPs used for scoring
CNT2 -The number of named alleles

It seems to me that plink might have interchanged CNT and CNT2 column but I do not understand what "number of named alleles" mean ? Also, the scoring is such, all my individuals are scored in the range of 0.017095 to 0.017999, isn't that a bit strange ?

Many thanks

Answer 1

[chrchang523]

Your score file should have lines looking like

rs4970405 G 0.0012

The second column names an allele which contributes to the score; CNT2 is the total number of named alleles actually observed. CNT is the number of alleles checked (the PLINK 1.07 documentation is incorrect here), so it's always at least as large as CNT2.

The small range is unsurprising if most of your scored variants have low minor allele frequencies. You can use the 'center' modifier to normalize them to have mean zero.

[NB]

Thank you for your comment. I didn't quite get your statement "You can use the 'center' modifier to normalize them to have mean zero." -> what do you mean by center modifier?

[chrchang523]

Instead of just "--score [filename]", you can type "--score [filename] center".

[NB]

Thank you, that helped but now some of my individuals have negative scores, does it mean that those individuals do not contribute to the diseased phenotype ?

[chrchang523]

If your score file is accurate, negative scores indicate lower risk and positive scores indicate higher risk.