|
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 |
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. 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:
|