R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

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> ### * <HEADER>
> ###
> 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("haplo.score-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('haplo.score')
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "Ginv"
> 
> ### * Ginv
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: Ginv
> ### Title: Compute Generalized Inverse of Input Matrix
> ### Aliases: Ginv
> 
> 
> ### ** Examples
> 
> ## Not run: 
> ##D save <- Ginv(x)
> ##D ginv.x <- save$Ginv
> ##D rank.x <- save$rank
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "allele.recode"
> 
> ### * allele.recode
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: allele.recode
> ### Title: Recode allele values to integer ranks
> ### Aliases: allele.recode
> 
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "banner"
> 
> ### * banner
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: banner
> ### Title: Print a nice banner
> ### Aliases: banner
> 
> 
> ### ** Examples
> 
> 
> banner("This is a pretty banner", banner.width=40, char.perline=30)
========================================

        This is a pretty banner

========================================

> 
> # ========================================
> #          This is a pretty banner
> # ========================================
> 
> 
> 
> cleanEx(); ..nameEx <- "gcode"
> 
> ### * gcode
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: gcode
> ### Title: Numeric Code for Genotypes
> ### Aliases: gcode
> 
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "geno.recode"
> 
> ### * geno.recode
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: geno.recode
> ### Title: Recode Genotypes
> ### Aliases: geno.recode
> 
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "haplo.em"
> 
> ### * haplo.em
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: haplo.em
> ### Title: EM Computation of Haplotype Probabilities
> ### Aliases: haplo.em
> 
> 
> ### ** Examples
> 
> ## Not run: 
> ##D haplo <- haplo.em(geno)
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "haplo.enum"
> 
> ### * haplo.enum
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: haplo.enum
> ### Title: Enumerate all possible pairs of haplotypes that are consistent
> ###   with a set of un-phased multilocus markers
> ### Aliases: haplo.enum
> 
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "haplo.hash"
> 
> ### * haplo.hash
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: haplo.hash
> ### Title: Integer Rank Codes for Haplotypes
> ### Aliases: haplo.hash
> 
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "haplo.score"
> 
> ### * haplo.score
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: haplo.score
> ### Title: Score Statistics for Association of Traits with Haplotypes
> ### Aliases: haplo.score
> 
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # For quantitative, normally distributed trait:
> ##D 
> ##D   haplo.score(y, geno, trait.type = "gaussian")
> ##D 
> ##D # For a  binary trait
> ##D 
> ##D   haplo.score(y, geno, trait.type = "binomial")
> ##D 
> ##D # For a binary trait, adjusted for sex and age:
> ##D 
> ##D   x <- cbind(sex, age)  
> ##D   haplo.score(y, geno, trait.type = "binomial", x.adj=x)
> ##D 
> ##D # For poisson trait:
> ##D 
> ##D   haplo.score(y, geno, trait.type="poisson", offset = personYears)
> ##D 
> ##D # For ordinal trait:
> ##D 
> ##D   haplo.score(y, geno, trait.type="ordinal")
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "haplo.score.glm"
> 
> ### * haplo.score.glm
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: haplo.score.glm
> ### Title: Compute haplotype score statistics for GLM
> ### Aliases: haplo.score.glm
> 
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "haplo.score.podds"
> 
> ### * haplo.score.podds
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: haplo.score.podds
> ### Title: Compute Haplotype Score Statistics for Ordinal Traits with
> ###   Proportional Odds Model
> ### Aliases: haplo.score.podds
> 
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "locator.haplo"
> 
> ### * locator.haplo
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: locator.haplo
> ### Title: Find Location from Mouse Clicks and Print Haplotypes on Plot
> ### Aliases: locator.haplo
> 
> 
> ### ** Examples
> 
> ## Not run: 
> ##D save <-  haplo.score(y, geno, trait.type = "binomial")
> ##D 
> ##D plot(save)
> ##D 
> ##D locator.haplo(save)
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "plot.haplo.score"
> 
> ### * plot.haplo.score
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: plot.haplo.score
> ### Title: Plot Haplotype Frequencies versus Haplotype Score Statistics
> ### Aliases: plot.haplo.score
> 
> 
> ### ** Examples
> 
> ## Not run: 
> ##D save <- haplo.score(y, geno, trait.type = "gaussian")
> ##D 
> ##D # Example illustrating generic plot function:
> ##D plot(save)
> ##D 
> ##D # Example illustrating specific method plot function:
> ##D plot.haplo.score(save)
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "print.haplo.score"
> 
> ### * print.haplo.score
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: print.haplo.score
> ### Title: Print a haplo.score object
> ### Aliases: print.haplo.score
> 
> 
> ### ** Examples
> 
> ## Not run: 
> ##D save <- haplo.score(y, geno, trait.type = "gaussian")
> ##D 
> ##D # Example illustrating generic print function:
> ##D print(save)
> ##D 
> ##D # Example illustrating specific method print function:
> ##D print.haplo.score(save)
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "ungcode"
> 
> ### * ungcode
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ungcode
> ### Title: Uncode Numeric Genotype Codes to Alleles
> ### Aliases: ungcode
> 
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  0.06 0.02 0.08 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')