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> ### > 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("qvalue-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('qvalue') > > assign(".oldSearch", search(), env = .CheckExEnv) > assign(".oldNS", loadedNamespaces(), env = .CheckExEnv) > cleanEx(); ..nameEx <- "qplot" > > ### * qplot > > flush(stderr()); flush(stdout()) > > ### Name: qplot > ### Title: Graphical display of qvalue objects > ### Aliases: qplot plot.qvalue > ### Keywords: misc > > ### ** Examples > > ## Not run: > ##D p <- scan(pvalues.txt) > ##D qobj <- qvalue(p) > ##D qplot(qobj) > ##D qwrite(qobj, filename=myresults.txt) > ##D > ##D # view plots for q-values between 0 and 0.3: > ##D plot(qobj, rng=c(0.0, 0.3)) > ## End(Not run) > > > > cleanEx(); ..nameEx <- "qsummary" > > ### * qsummary > > flush(stderr()); flush(stdout()) > > ### Name: qsummary > ### Title: Display qvalue object > ### Aliases: qsummary summary.qvalue > ### Keywords: misc > > ### ** Examples > > ## Not run: > ##D qobj <- qvalue(p) > ##D print(qobj) > ##D summary(qobj, cuts=c(0.01, 0.05)) > ## End(Not run) > > > > cleanEx(); ..nameEx <- "qvalue" > > ### * qvalue > > flush(stderr()); flush(stdout()) > > ### Name: qvalue > ### Title: Estimate the q-values for a given set of p-values > ### Aliases: qvalue > ### Keywords: misc > > ### ** Examples > > ## Not run: > ##D p <- scan("pvalues.txt") > ##D qobj <- qvalue(p) > ##D qplot(qobj) > ##D qwrite(qobj, filename="myresults.txt") > ##D > ##D qobj <- qvalue(p, lambda=0.5, robust=TRUE) > ##D qobj <- qvalue(p, fdr.level=0.05, pi0.method="bootstrap") > ## End(Not run) > > > > cleanEx(); ..nameEx <- "qvalue.gui" > > ### * qvalue.gui > > flush(stderr()); flush(stdout()) > > ### Name: qvalue.gui > ### Title: A graphical user interface for QValue > ### Aliases: qvalue.gui > ### Keywords: misc > > ### ** Examples > > ## Not run: > ##D qvalue.gui() > ## End(Not run) > > > > cleanEx(); ..nameEx <- "qwrite" > > ### * qwrite > > flush(stderr()); flush(stdout()) > > ### Name: qwrite > ### Title: Write the results of the q-value object qobj to a file > ### Aliases: qwrite > ### Keywords: misc > > ### ** Examples > > ## Not run: > ##D p <- scan("pvalues.txt") > ##D qobj <- qvalue(p) > ##D qplot(qobj) > ##D qwrite(qobj, filename="myresults.txt") > ## End(Not run) > > > > ### *