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("stepwise-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('stepwise') > > assign(".oldSearch", search(), env = .CheckExEnv) > assign(".oldNS", loadedNamespaces(), env = .CheckExEnv) > cleanEx(); ..nameEx <- "maxchi" > > ### * maxchi > > flush(stderr()); flush(stdout()) > > ### Name: maxchi > ### Title: Stepwise detection of recombination breakpoints using MaxChi > ### Aliases: maxchi > ### Keywords: htest > > ### ** Examples > demo(maxchi) demo(maxchi) ---- ~~~~~~ > inputFile <- system.file("data", "simulinfile", package = "stepwise") > breaks <- c(531, 616, 810) > WinHalfWidth <- 30 > permReps <- 10 > a <- maxchi(inputFile, breaks, WinHalfWidth, permReps) > summary.maxchi(a) -------------------------------------------------- There were 39 site-specific MaxChi statistics significant at the 10 percent level (90th percentile = 17.067, 95th percentile = 17.067): Number Location MaxChi pairs 1 342 17.143* (sample15__:sample28__) (sample16__:sample28__) 2 463 18.261* (sample20__:sample24__) 3 470 18.261* (sample20__:sample24__) 4 531 20.000* (sample17__:sample27__) 5 548 20.000* (sample17__:sample27__) 6 549 20.000* (sample17__:sample27__) 7 556 20.000* (sample17__:sample27__) 8 558 18.261* (sample17__:sample27__) 9 564 18.261* (sample17__:sample27__) 10 568 18.261* (sample17__:sample27__) 11 573 18.261* (sample17__:sample27__) 12 588 18.373* (sample17__:sample20__) 13 604 18.373* (sample17__:sample20__) 14 616 20.000* (sample19__:sample30__) 15 620 18.468* (sample19__:sample30__) 16 622 18.468* (sample19__:sample30__) 17 633 17.330* (sample21__:sample30__) 18 637 17.330* (sample21__:sample30__) 19 644 17.330* (sample21__:sample30__) 20 649 17.330* (sample21__:sample30__) 21 752 17.143* (sample29__:sample30__) 22 753 17.143* (sample29__:sample30__) 23 756 17.143* (sample29__:sample30__) 24 805 17.376* (sample3___:sample8___) (sample3___:sample9___) 25 807 19.461* (sample3___:sample8___) (sample3___:sample9___) 26 810 24.310* (sample3___:sample8___) (sample3___:sample9___) 27 811 19.461* (sample3___:sample8___) (sample3___:sample9___) (sample3___:sample11__) (sample3___:sample15__) (sample3___:sample16__) 28 815 19.461* (sample3___:sample8___) (sample3___:sample9___) (sample3___:sample11__) (sample3___:sample15__) (sample3___:sample16__) 29 818 17.143* (sample3___:sample8___) (sample3___:sample9___) (sample3___:sample11__) (sample3___:sample15__) (sample3___:sample16__) 30 819 17.330* (sample3___:sample14__) (sample3___:sample27__) 31 825 17.330* (sample3___:sample14__) (sample3___:sample27__) 32 826 19.200* (sample3___:sample14__) (sample3___:sample27__) 33 827 21.172* (sample3___:sample14__) (sample3___:sample27__) 34 828 19.200* (sample4___:sample14__) (sample4___:sample27__) 35 832 21.172* (sample4___:sample14__) (sample4___:sample27__) 36 834 21.172* (sample4___:sample13__) (sample4___:sample14__) (sample4___:sample27__) 37 844 21.172* (sample4___:sample13__) (sample4___:sample14__) (sample4___:sample27__) 38 854 18.373* (sample13__:sample18__) (sample14__:sample18__) (sample18__:sample27__) 39 858 18.373* (sample1___:sample13__) (sample1___:sample14__) (sample1___:sample27__) (sample4___:sample13__) (sample4___:sample14__) (sample4___:sample27__) (sample5___:sample13__) (sample5___:sample14__) (sample5___:sample27__) (sample6___:sample13__) (sample6___:sample14__) (sample6___:sample27__) (sample7___:sample13__) (sample7___:sample14__) (sample7___:sample27__) -------------------------------------------------- Notes - "Location" is the polymorphic site just before the proposed breakpoint. - MaxChi statistics significant at the 5 percent level indicated by a * > > > cleanEx(); ..nameEx <- "phylpro" > > ### * phylpro > > flush(stderr()); flush(stdout()) > > ### Name: phylpro > ### Title: Stepwise detection of recombination breakpoints using Phylpro > ### Aliases: phylpro > ### Keywords: htest > > ### ** Examples > demo(phylpro) demo(phylpro) ---- ~~~~~~~ > inputFile <- system.file("data", "simulinfile", package = "stepwise") > breaks <- c(548, 735, 832) > WinHalfWidth <- 30 > permReps <- 10 > b <- phylpro(inputFile, breaks, WinHalfWidth, permReps) > summary.phylpro(b) -------------------------------------------------- There were 18 site-specific Minimum Correlation statistics significant at the 10 percent level (10th percentile = -0.487, 5th percentile = 0.000): Number Location MinCor targets 1 513 -0.549* sample28__ 2 526 -0.656* sample28__ 3 527 -0.627* sample28__ 4 528 -0.583* sample28__ 5 531 -0.648* sample28__ 6 548 -0.696* sample28__ 7 549 -0.691* sample28__ 8 556 -0.684* sample28__ 9 558 -0.635* sample28__ 10 564 -0.631* sample28__ 11 568 -0.625* sample28__ 12 573 -0.641* sample28__ 13 576 -0.528* sample28__ 14 579 -0.539* sample28__ 15 583 -0.536* sample28__ 16 588 -0.616* sample28__ 17 604 -0.509* sample28__ 18 735 -0.492* sample29__ -------------------------------------------------- Notes - "Location" is the polymorphic site just before the proposed breakpoint. - MinCor statistics significant at the 5 percent level indicated by a * > > > cleanEx(); ..nameEx <- "stepwise.seqs" > > ### * stepwise.seqs > > flush(stderr()); flush(stdout()) > > ### Name: stepwise.seqs > ### Title: Simulated sequence alignment from the stepwise package > ### Aliases: stepwise.seqs stepwise > ### Keywords: datasets > > ### ** Examples > > data(stepwise.seqs) > dim(stepwise.seqs) # 30 x 1000 NULL > ## Not run: > ##D # write the 30 sequences to a Phylip-format input file > ##D cat(paste(nrow(stepwise.seqs),ncol(stepwise.seqs),"\n"), > ##D file="stepwise.phy") > ##D write.table(stepwise.seqs,file="stepwise.phy",append=TRUE,quote=FALSE, > ##D sep="", row.names=TRUE,col.names=FALSE) > ## End(Not run) > > > > cleanEx(); ..nameEx <- "summary.maxchi" > > ### * summary.maxchi > > flush(stderr()); flush(stdout()) > > ### Name: summary.maxchi > ### Title: Summary of a maxchi object > ### Aliases: summary.maxchi > ### Keywords: print > > ### ** Examples > demo(maxchi) demo(maxchi) ---- ~~~~~~ > inputFile <- system.file("data", "simulinfile", package = "stepwise") > breaks <- c(531, 616, 810) > WinHalfWidth <- 30 > permReps <- 10 > a <- maxchi(inputFile, breaks, WinHalfWidth, permReps) > summary.maxchi(a) -------------------------------------------------- There were 43 site-specific MaxChi statistics significant at the 10 percent level (90th percentile = 16.484, 95th percentile = 16.484): Number Location MaxChi pairs 1 342 17.143* (sample15__:sample28__) (sample16__:sample28__) 2 453 16.596* (sample20__:sample24__) 3 463 18.261* (sample20__:sample24__) 4 470 18.261* (sample20__:sample24__) 5 528 16.705* (sample17__:sample27__) 6 531 20.000* (sample17__:sample27__) 7 548 20.000* (sample17__:sample27__) 8 549 20.000* (sample17__:sample27__) 9 556 20.000* (sample17__:sample27__) 10 558 18.261* (sample17__:sample27__) 11 564 18.261* (sample17__:sample27__) 12 568 18.261* (sample17__:sample27__) 13 573 18.261* (sample17__:sample27__) 14 576 16.596* (sample17__:sample27__) 15 588 18.373* (sample17__:sample20__) 16 604 18.373* (sample17__:sample20__) 17 616 20.000* (sample19__:sample30__) 18 618 16.705* (sample19__:sample30__) 19 620 18.468* (sample19__:sample30__) 20 622 18.468* (sample19__:sample30__) 21 633 17.330* (sample21__:sample30__) 22 637 17.330* (sample21__:sample30__) 23 644 17.330* (sample21__:sample30__) 24 649 17.330* (sample21__:sample30__) 25 752 17.143* (sample29__:sample30__) 26 753 17.143* (sample29__:sample30__) 27 756 17.143* (sample29__:sample30__) 28 805 17.376* (sample3___:sample8___) (sample3___:sample9___) 29 807 19.461* (sample3___:sample8___) (sample3___:sample9___) 30 810 24.310* (sample3___:sample8___) (sample3___:sample9___) 31 811 19.461* (sample3___:sample8___) (sample3___:sample9___) (sample3___:sample11__) (sample3___:sample15__) (sample3___:sample16__) 32 815 19.461* (sample3___:sample8___) (sample3___:sample9___) (sample3___:sample11__) (sample3___:sample15__) (sample3___:sample16__) 33 818 17.143* (sample3___:sample8___) (sample3___:sample9___) (sample3___:sample11__) (sample3___:sample15__) (sample3___:sample16__) 34 819 17.330* (sample3___:sample14__) (sample3___:sample27__) 35 825 17.330* (sample3___:sample14__) (sample3___:sample27__) 36 826 19.200* (sample3___:sample14__) (sample3___:sample27__) 37 827 21.172* (sample3___:sample14__) (sample3___:sample27__) 38 828 19.200* (sample4___:sample14__) (sample4___:sample27__) 39 832 21.172* (sample4___:sample14__) (sample4___:sample27__) 40 834 21.172* (sample4___:sample13__) (sample4___:sample14__) (sample4___:sample27__) 41 844 21.172* (sample4___:sample13__) (sample4___:sample14__) (sample4___:sample27__) 42 854 18.373* (sample13__:sample18__) (sample14__:sample18__) (sample18__:sample27__) 43 858 18.373* (sample1___:sample13__) (sample1___:sample14__) (sample1___:sample27__) (sample4___:sample13__) (sample4___:sample14__) (sample4___:sample27__) (sample5___:sample13__) (sample5___:sample14__) (sample5___:sample27__) (sample6___:sample13__) (sample6___:sample14__) (sample6___:sample27__) (sample7___:sample13__) (sample7___:sample14__) (sample7___:sample27__) -------------------------------------------------- Notes - "Location" is the polymorphic site just before the proposed breakpoint. - MaxChi statistics significant at the 5 percent level indicated by a * > > > cleanEx(); ..nameEx <- "summary.phylpro" > > ### * summary.phylpro > > flush(stderr()); flush(stdout()) > > ### Name: summary.phylpro > ### Title: Summary of a phylpro object > ### Aliases: summary.phylpro > ### Keywords: print > > ### ** Examples > demo(phylpro) demo(phylpro) ---- ~~~~~~~ > inputFile <- system.file("data", "simulinfile", package = "stepwise") > breaks <- c(548, 735, 832) > WinHalfWidth <- 30 > permReps <- 10 > b <- phylpro(inputFile, breaks, WinHalfWidth, permReps) > summary.phylpro(b) -------------------------------------------------- There were 12 site-specific Minimum Correlation statistics significant at the 10 percent level (10th percentile = -0.562, 5th percentile = 0.000): Number Location MinCor targets 1 526 -0.656* sample28__ 2 527 -0.627* sample28__ 3 528 -0.583* sample28__ 4 531 -0.648* sample28__ 5 548 -0.696* sample28__ 6 549 -0.691* sample28__ 7 556 -0.684* sample28__ 8 558 -0.635* sample28__ 9 564 -0.631* sample28__ 10 568 -0.625* sample28__ 11 573 -0.641* sample28__ 12 588 -0.616* sample28__ -------------------------------------------------- Notes - "Location" is the polymorphic site just before the proposed breakpoint. - MinCor statistics significant at the 5 percent level indicated by a * > > > ### *