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
1 answer
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.
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written
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chrchang523
Instead of just "--score [filename]", you can type "--score [filename] center".
If your score file is accurate, negative scores indicate lower risk and positive scores indicate higher risk.
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