--score precision error

[smlmbrt]

Hi there, I've noticed that the SUM and AVG are missing a decimal place of precision when you use the plink2 --score command. You can see it clearly with a scoring file with 1 variant:

ID      effect_allele   pgs_af
22:20441888:T:C T       -4.997371e-05

And the results scoring it on HGDP:

#IID    population      latitude        longitude       region  ALLELE_CT       DENOM   NAMED_ALLELE_DOSAGE_SUM pgs_af_AVG      pgs_af_SUM
HGDP00001       Brahui  30.5    66.5    CENTRAL_SOUTH_ASIA      2       2       1       -2.49869e-05    -4.99737e-05
HGDP00003       Brahui  30.5    66.5    CENTRAL_SOUTH_ASIA      2       2       0       0       0
HGDP00005       Brahui  30.5    66.5    CENTRAL_SOUTH_ASIA      2       2       1       -2.49869e-05    -4.99737e-05
HGDP00007       Brahui  30.5    66.5    CENTRAL_SOUTH_ASIA      2       2       2       -4.99737e-05    -9.99474e-05
[... the rest are omitted]

The possible values of SUM should be [0, -4.997371e-05, -9.994742e-05], but they are [0, 4.99737e-05, -9.99474e-05]. I get the same results in v1.90b7, v2.00a3.3, and v2.00a4. This didn't change when I provided the weight as -0.00004997371 either.

[chrchang]

Not a bug. Practically all plink2 commands print floating-point values to 6 decimal places; printing to "full precision" would inflate file sizes while adding negligible scientific value. The source code is available if you actually need more digits of precision to be printed here.

[smlmbrt]

@chrchang, thanks for the explanation! So if I understand correctly the full precision is used for the calculation internally but it just prints to 6 decimal places?

[chrchang]

That is correct.