Nothing
#just wait for a key before continuing
readkey <- function()
{
cat ("Press [enter] to continue")
line <- readline()
}
#' Demo of fastcmh
#'
#' This function runs a demo for fastcmh, by first creating a sample data set
#' and then running fastcmh on this data set.
#'
#' @param saveToFolder A flag indicating whether or not the data files created
#' for the demo should be saved to file. The default is \code{FALSE}, i.e. no
#' files are saved to the folder. The only reason to save demo data to a
#' folder is for the user to be able to have a look at the files after the
#' demo.
#'
#' @param folder The folder in which the data for the demo will be saved.
#' Default is the current directory, \code{"./"}. The demo data will created
#' in \code{folder/data} and the results will be saved in
#' \code{folder/results} as an RData file.
#'
#' @section Details:
#' This function will first create a sample data set in \code{folder/data},
#' and will then run \code{runfastcmh} on this data set, before saving the
# results in \code{folder/results}. The method runs in several steps, with
#' each step showing the R code that can be used to do the step, then running
#' that R code, and then waiting for the user to press enter before moving
#' onto the next step. If \code{saveToFolder=FALSE}, (default) then no files
#' are saved and all the results are kept in memory.
#'
#' @section See Also:
#' \code{\link{runfastcmh}}
#'
#' @examples
#' demofastcmh()
#' @export
demofastcmh <- function(saveToFolder=FALSE, folder=NULL){
#the amount of delay, when a sleep delay was used instead of readkey()
sleepDelay <- 2
#check saveAllPvals:
if (is.null(saveToFolder)){
saveToFolder <- FALSE
}
if(isTRUE(saveToFolder)){
saveToFolder <- TRUE
} else {
saveToFolder <- FALSE
}
#check saveFolder:
if (is.null(folder)){
folder <- "./fastcmhdemo/"
}
#normalise the path
# folder <- normalizePath(folder)
folder <- fixSeparator(folder)
#check it is a folder
folder <- checkIsFolder(folder)
cat("\n")
cat("====================================================\n")
cat("fastcmh Demo:\n")
cat("====================================================\n\n")
#creating folder
if (saveToFolder==TRUE){
cat("Creating folders for demo: ", folder, "\n", sep="")
folder <- checkFolderExists(folder)
#create data folder and results folder
datafolder <- paste0(folder, "data")
datafolder <- checkFolderExists(datafolder)
resultsfolder <- paste0(folder, "results")
resultsfolder <- checkFolderExists(resultsfolder)
#add a delay
cat("\n")
# Sys.sleep(sleepDelay)
readkey();
cat("----------------------------------------------------\n\n")
cat("Step 1: Creating data files for demo \n", sep="")
cat("**(Run command)**\n")
cat("> makefastcmhdata(\"", datafolder, "\", showOutput=TRUE)\n\n", sep="")
readkey();
makefastcmhdata(datafolder, showOutput=TRUE)
cat("\n\n")
cat("Sample data created in ", datafolder, "\n\n", sep="")
readkey();
cat("\n\n----------------------------------------------------\n")
cat("\n")
cat("Step 2: Now running fastcmh, and saving results to file\n")
cat("**(Run command)**\n")
cat("> runfastcmh(folder=\"", datafolder, ", saveToFile=TRUE, saveFolder=\"", resultsfolder, "\")\n\n", sep="")
readkey();
#Do fastcmh
runfastcmh(folder=datafolder, saveToFile=TRUE, saveFolder=resultsfolder)
resultsfile <- paste0(resultsfolder, "fastcmhresults.RData")
cat("\n\n----------------------------------------------------\n")
cat("\n")
cat("Step 3: Inspect the results\n")
cat("**(Run commands)**\n")
cat("> load(\"", resultsfile, "\")\n", sep="")
cat("> str(fastcmhresults)\n\n", sep="")
fastcmhresults <- runfastcmh(folder=datafolder, saveToFile=FALSE)
print(str(fastcmhresults))
readkey();
} else {
cat("----------------------------------------------------\n\n")
cat("Step 1: Creating data files for demo \n", sep="")
cat("**(Run command)**\n")
cat("> makefastcmhdata(folder=/data/, showOutput=TRUE)\n\n", sep="")
cat("( files can be found in fastcmh/inst/extdata/ )\n\n")
readkey();
mylist <- makefastcmhdata(showOutput=TRUE, saveToList=TRUE)
readkey();
cat("\n\n----------------------------------------------------\n")
cat("\n")
cat("Step 2: Now running fastcmh, and saving results to list\n")
cat("**(Run command)**\n")
cat("> fastcmhresults <- runfastcmh(folder=/data/, saveToFile=FALSE)\n\n", sep="")
fastcmhresults <- runfastcmh(folder="/data/", saveToFile=FALSE)
readkey();
cat("\n\n----------------------------------------------------\n")
cat("\n")
cat("Step 3: Inspect the results\n")
cat("**(Run commands)**\n")
cat("> str(fastcmhresults)\n\n", sep="")
print(str(fastcmhresults))
readkey();
}
cat("\n\n----------------------------------------------------\n")
cat("Step 4: Or, access the results directly\n")
cat("\n\n")
cat("The data frame of significant intervals (filtered) can be found using:\n")
cat("**(Run command)**\n")
cat("> fastcmhresults$sig\n", sep="")
cat("\n")
print(fastcmhresults$sig)
cat("\n")
cat("In other words, ", sep="")
if (nrow(fastcmhresults$sig)==1){
cat("the only ", sep="")
} else {
cat("the first", sep="")
}
cat("significant interval is [", as.numeric(fastcmhresults$sig[1]), ", ", as.numeric(fastcmhresults$sig[2]), "],\n", sep="")
cat("and the confounded interval [200, 203] is not found/is ignored.\n")
cat("\n\n")
cat("====================================================\n")
cat("End of Demo\n")
cat("====================================================\n\n")
}
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