[Genabel-commits] r1192 - tutorials/GenABEL_general

[noreply at r-forge.r-project.org]

Author: yurii
Date: 2013-04-16 21:07:09 +0200 (Tue, 16 Apr 2013)
New Revision: 1192

Modified:
   tutorials/GenABEL_general/fetchData.Rnw
Log:
changes so that user can simply copy the code for fetching the data

Modified: tutorials/GenABEL_general/fetchData.Rnw
===================================================================
--- tutorials/GenABEL_general/fetchData.Rnw	2013-04-16 16:30:29 UTC (rev 1191)
+++ tutorials/GenABEL_general/fetchData.Rnw	2013-04-16 19:07:09 UTC (rev 1192)
@@ -1,20 +1,29 @@
 \section{Download necessary files}
-This code needs to be run prior to other parts of tutorial.
 
-It kills the 'RData' directory if it is there (danger! danger!) to make all tests
-clean. 
+This code needs to be run prior to other parts of tutorial. We reccommend that
+prior to any actions you create a new directory, say, 'exercisesGenABEL', to
+keep all of your working tutorial files there.
 
-<<>>=
+Start R and make sure that your working directory is set to a proper location.
+Your current working directory can be queried by command 'getwd()'.
+Use 'setwd' command to set the working directory.
+
+The next lines of code kill the 'RData' directory if it is present in your
+working directory (danger! danger!) to make new clean data installation. Paste
+this code into R:
+
+\begin{verbatim}
 unlink("RData",recursive=TRUE,force=TRUE)
 dir.create("RData")
+\end{verbatim}
+<<echo=FALSE>>=
+unlink("RData",recursive=TRUE,force=TRUE)
+dir.create("RData")
 @ 
 
-Now, fetch the necessary data from the server
-{\bf Would be nice to have this thing as a 'code' plate so people can
-  copy-paste the code without the need to delete '+'ses}
-
-Define download procedure
-<<>>=
+Now, fetch the necessary data from the server. First, define the download
+procedure
+\begin{verbatim}
 myDownloads <- function(baseUrl,baseLocal,files) {
 for (cFile in files) {
     cFileUrl <- paste(baseUrl,cFile,sep="")
@@ -26,11 +35,23 @@
       stop(paste("can not download",cFileUrl,"into",cFileLocal,":",tryDownload))
   }
 }
+\end{verbatim}
+<<echo=FALSE>>=
+myDownloads <- function(baseUrl,baseLocal,files) {
+for (cFile in files) {
+    cFileUrl <- paste(baseUrl,cFile,sep="")
+    cFileLocal <- paste(baseLocal,cFile,sep="")
+    tryDownload <- try( 
+                       download.file(url=cFileUrl,destfile=cFileLocal) 
+                       )
+    if ( is(tryDownload,"try-error") ) 
+      stop(paste("can not download",cFileUrl,"into",cFileLocal,":",tryDownload))
+  }
+}
 @ 
 
-Download data files:
-
-<<>>=
+Second, download data files:
+\begin{verbatim}
 baseUrl <- "http://www.genabel.org/sites/default/files/data/"
 baseLocal <- "RData/"
 dataFiles <- c(
@@ -49,16 +70,37 @@
            "emap0.dat",
            "phe0.dat",
            "ImputedDataAnalysis.RData")
-
 myDownloads(baseUrl,baseLocal,dataFiles)
+\end{verbatim}
+<<echo=FALSE>>=
+baseUrl <- "http://www.genabel.org/sites/default/files/data/"
+baseLocal <- "RData/"
+dataFiles <- c(
+           "assocbase.RData",
+           "popdat.RData",
+           "mach1.out.mlinfo",
+           "mach1.mldose.fvi",
+           "mach1.mldose.fvd",
+           "rcT.PHE",
+           "gen0.illu",
+           "gen0.illuwos",
+           "gen0.tped",
+           "gen0.tfam",
+           "gen0.ped",
+           "map0.dat",
+           "emap0.dat",
+           "phe0.dat",
+           "ImputedDataAnalysis.RData")
+myDownloads(baseUrl,baseLocal,dataFiles)
 @ 
 
-Special case of figure(s):
-
-<<>>=
+<<echo=FALSE>>=
+#Special case of figure(s), not shown to user
 baseLocal <- ""
 figuresFiles <- c(
            "gwaa-data-class.pdf"
            )
 myDownloads(baseUrl,baseLocal,figuresFiles)
 @ 
+
+That's it! - now you are fully set to start with the \texttt{GenABEL} tutorial!