R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. > ### *
> ### > attach(NULL, name = "CheckExEnv") > assign(".CheckExEnv", as.environment(2), pos = length(search())) # base > ## add some hooks to label plot pages for base and grid graphics > setHook("plot.new", ".newplot.hook") > setHook("persp", ".newplot.hook") > setHook("grid.newpage", ".gridplot.hook") > > assign("cleanEx", + function(env = .GlobalEnv) { + rm(list = ls(envir = env, all.names = TRUE), envir = env) + RNGkind("default", "default") + set.seed(1) + options(warn = 1) + delayedAssign("T", stop("T used instead of TRUE"), + assign.env = .CheckExEnv) + delayedAssign("F", stop("F used instead of FALSE"), + assign.env = .CheckExEnv) + sch <- search() + newitems <- sch[! sch %in% .oldSearch] + for(item in rev(newitems)) + eval(substitute(detach(item), list(item=item))) + missitems <- .oldSearch[! .oldSearch %in% sch] + if(length(missitems)) + warning("items ", paste(missitems, collapse=", "), + " have been removed from the search path") + }, + env = .CheckExEnv) > assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now > assign("ptime", proc.time(), env = .CheckExEnv) > grDevices::postscript("impute-Examples.ps") > assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv) > options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly")) > options(warn = 1) > library('impute') > > assign(".oldSearch", search(), env = .CheckExEnv) > assign(".oldNS", loadedNamespaces(), env = .CheckExEnv) > cleanEx(); ..nameEx <- "impute.knn" > > ### * impute.knn > > flush(stderr()); flush(stdout()) > > ### Name: impute.knn > ### Title: A function to impute missing expression data > ### Aliases: impute.knn > ### Keywords: data > > ### ** Examples > > data(khanmiss) > khan.expr <- khanmiss[-1, -(1:2)] > ## > ## First example > ## > if(exists(".Random.seed")) rm(.Random.seed) > khan.imputed <- impute.knn(as.matrix(khan.expr)) Cluster size 2308 broken into 1448 860 Done cluster 1448 Done cluster 860 > ## > ## khan.imputed$data should now contain the imputed data matrix > ## khan.imputed$rng.seed should contain the random number seed used > ## in imputation. In the above invocation, it is the default seed. > ## > attr(khan.imputed, "rng.seed") # should be 362436069 [1] 362436069 > attr(khan.imputed, "rng.state") # should be NULL NULL > ## > ## Second example > ## > set.seed(12345) > saved.state <- .Random.seed > khan.imputed <- impute.knn(as.matrix(khan.expr)) Cluster size 2308 broken into 1448 860 Done cluster 1448 Done cluster 860 > # Assuming all goes well with no guarantees in case of error... > .Random.seed <- attr(khan.imputed, "rng.state") > sum(saved.state - attr(khan.imputed, "rng.state")) # should be zero! [1] 0 > save(khan.imputed, file="khanimputation.Rda") > > > > ### *