Error: --score takes at most three numeric parameters.

Question

[Travis]

I used the --score flag to calculate a polygenic risk score from dosage data. The arguments "1 2 3" are the columns for SNP ID, risk allele, and the absolute value of beta for the risk allele, respectively. These are the only columns in the file snp_list. My script is:

plink2 \

--pfile mydata \

--score snp_list 1 2 3 header sum no-mean-imputation \

--memory 4000 \

--threads 5

This returns "Error: --score takes at most three numeric parameters." Any suggestions? Thanks.

Answer 1

[chrchang523]

Sorry about the inappropriate error message; I'll fix that in the next build. The actual issue is that plink2 --score replaces the 'sum' modifier with direct control over the output columns. "plink2 --help score" has the following text toward the end:

  The main report supports the following column sets:
    maybefid: FID, if that column was in the input.
    fid: Force FID column to be written even when absent in the input.
    (IID are always present, and positioned here.)
    maybesid: SID, if that column was in the input.
    sid: Force SID column to be written even when absent in the input.
    pheno1: First active phenotype.
    phenos: All active phenotypes, if any.
    nmissallele: Number of nonmissing alleles.
    denom: Denominator of score average (equal to nmissallele value when
           'no-mean-imputation' specified).
    dosagesum: Sum of named allele dosages.
    scoreavgs: Score averages.
    scoresums: Score sums.
  The default is maybefid,maybesid,phenos,nmissallele,dosagesum,scoreavgs.

Note the "scoresums" option at the bottom. This means that if you add "cols=+scoresums" to your --score invocation, that will add the sum column you're looking for.

Answer 2

[Travis]

The modifiers 'sum' and 'no-mean-imputation' are mutually exclusive according to the documentation.