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S: 22 Oct 2024 (b.7.7) D: 22 Oct 2024 Main functions (--distance...) (--make-grm-bin...) (--ibs-test...) (--assoc, --model) (--mh, --mh2, --homog) (--assoc, --gxe) (--linear, --logistic) Core algorithms Quick index search |
Allelic scoring--score <filename> [variant ID col.] [allele col.] [score col.] ['header'] [{sum | no-sum}] [{no-mean-imputation | center}] ['include-cnt'] ['double-dosage'] It's useful at times to apply a simple linear scoring system to all your genotypes; for example, this approach can be used to estimate genetic load, or apply additive effect estimates for a quantitative trait. The --score flag performs this function, writing results to plink.profile (unless --q-score-range is also present; see below). The input file should have one line per scored variant. By default, the variant ID is read from column 1, an allele code is read from the following column, and the score associated with the named allele is read from the column after the allele column; you can change these positions by passing column numbers to --score. E.g. --score my.scores 2 4 reads variant IDs from column 2, allele codes from column 4, and scores from column 5, while --score my.scores 3 2 1 reads variant IDs from column 3, allele codes from column 2, and scores from column 1. In addition,
--score can be used on --lasso's output as follows: plink --bfile mydata --score plink.lasso 2 header sum --q-score-range <range file> <data file> [variant ID col.] [data col.] ['header'] To apply --score to subset(s) of variants in the primary score list based on ranges of some key quantity (e.g. p-value), you can use --q-score-range. The first parameter should be the name of a file with range labels in the first column, lower bounds in the second column, and upper bounds in the third column, such as S1 0.00 0.01 (Lines with too few entries or nonnumeric values in the second or third column are ignored, so it's generally safe to include a header line in this file.) This would cause three score reports to be generated: plink.S1.profile would only consider variants with key quantity values in [0, 0.01], plink.S2.profile would only consider [0, 0.2], and plink.S3.profile would only consider [0.1, 0.5]. The second file should contain a variant ID and the key quantity on each nonempty line (except possibly the first). By default, variant IDs are assumed to be in column 1 and the quantity in the following column; you can change these positions in the same way as with --score. The 'header' modifier causes the first nonempty line of the second file to be skipped. |