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S: 11 Dec 2023 (b7.2) D: 11 Dec 2023 Main functions (--distance...) (--make-grm-bin...) (--ibs-test...) (--assoc, --model) (--mh, --mh2, --homog) (--assoc, --gxe) (--linear, --logistic) Core algorithms Quick index search |
R plugin functions--R <R script filename> ['debug'] (Not supported on Windows.) PLINK is designed to interoperate well with R: almost all built-in commands generate tabular reports that are easy to load and postprocess in it. With the Rserve package (preferably version 1.7 or later) and PLINK's --R flag, you can also apply R functions directly to PLINK binary data, without the need to write your own I/O code. --R loads the given R script, which must have a function of the form Rplink <- function(PHENO,GENO,CLUSTER,COVAR) where
(N is the number of samples with nonmissing phenotype values (after filtering); C, which can be zero, is the number of covariates; and m is the number of variants in the current data block, which is usually smaller than the total number in the dataset.) For each variant, PLINK expects this function to return a numeric vector of values of the form c(length(r), r) where the vectors are permitted to have different lengths. The PLINK 1.07 documentation contains several detailed examples. If this basic interface is insufficient for your needs, you may find the PLINK/SEQ R package to be more helpful. On a normal --R run, results are written to plink.auto.R. If you want to look at the R commands PLINK sends, add the 'debug' modifier; this causes them to be logged to plink.debug.R (without being executed). Connecting elsewhere--R-port <port number> --R-host <host> By default, --R tries to connect to a local Rserve instance on port 6311. You can change this as follows:
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