[Patchwork-commits] r177 - www

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

Author: sebastian_d
Date: 2013-06-24 14:07:52 +0200 (Mon, 24 Jun 2013)
New Revision: 177

Modified:
   www/TAPS_exec.php
   www/TAPS_inst.php
Log:
Homepage added info on TAPS execution

Modified: www/TAPS_exec.php
===================================================================
--- www/TAPS_exec.php	2013-06-19 09:09:55 UTC (rev 176)
+++ www/TAPS_exec.php	2013-06-24 12:07:52 UTC (rev 177)
@@ -7,7 +7,7 @@
 <h4>TAPS_plot()</h4>
 
 TAPS_plot() is a function that visualizes allele-specific copy numbers from microarray
-data of tumors. It can either be run in a directory containing multiple sample folder or
+data of tumors. It can either be run in a directory containing multiple sample folders or
 pointing to a specific sample, which would quite simply be a folder containing no subfolders
 and ideally the files needed to execute.
 <br /><br />
@@ -48,12 +48,27 @@
 </pre>
 
 The only thing TAPS_plot() needs is the directory argument. If, as mentioned above, you have
-a folder containing several sample folders then specifying "directory" to that top folder
-will execute all the sample subfolders. If you only have one sample folder then specifying
-"directory" to that sample folder will execute it. Note that specifying any folder containing
-subfolders will interpret the subfolders as the sample folders.
+a folder containing several sample folders then specifying "directory" to that main folder
+will execute all the sample subfolders.
+
+<img id="main" src="css/img/Main_folder.png" alt="Main folder" title="Main folder input"
+ style="border:1px solid black"><br /><br />
+
+Specifying "directory" to a single sample folder will execute only that sample. For example
+the folders Sample1 and Sample2.
 <br /><br />
+<b>Nexus</b><br />
+ <img id="Nexus" src="css/img/Nexus.png" alt="Nexus" title="Nexus input"
+ style="border:1px solid black">
+ <br />
+<b>ChAS</b><br />
+<img id="Chas" src="css/img/Chas.png" alt="Chas" title="Chas input"
+style="border:1px solid black">
+<br /><br />
 
+Note that specifying any folder containing subfolders will interpret the subfolders as the sample folders.
+<br /><br />
+
 Here is an example execution of TAPS_plot() using the current working directory, ".", as input
 and all the output left for display. The 6295 sample was processed from Nexus. TAPS_plot()
 processed sample 6295 completely then went into the next folder, "NonSampleFolder", which is not
@@ -91,13 +106,13 @@
 
 <h4>TAPS_call()</h4>
 
-The function TAPS_call() uses the relationship between logRatio
+The function TAPS_call() uses the relationship between log-ratio
 and allelic imbalance to assign copy number and allele ratio for each segment.
 <br /><br />
 
 TAPS_plot() must have been executed before TAPS_call() can be. This is because the .Rdata files
-generated during TAPS_plot() will be automatically read by TAPS_call() and you need the plots
-generated by TAPS_plot() to give TAPS_call() meaningful input.  
+generated during TAPS_plot() will be automatically read by TAPS_call() and you need to interpret the plots
+generated by TAPS_plot() to be able to give TAPS_call() meaningful input.  
 <br /><br />
 
 TAPS_call() also has "directory" as its main argument, the parameters are read from the file
@@ -106,7 +121,7 @@
 for that sample to SampleData.txt and specify that sample using the "directory" argument of TAPS_call().
 <br /><br />
 
-An example run of TAPS_call(),where "mainsamplefolder" contains SampleData.txt: <br />
+An example run of TAPS_call(), where "mainsamplefolder" contains SampleData.txt: <br />
 
 <pre>
 	TAPS_call(directory="path/to/mainsamplefolder")

Modified: www/TAPS_inst.php
===================================================================
--- www/TAPS_inst.php	2013-06-19 09:09:55 UTC (rev 176)
+++ www/TAPS_inst.php	2013-06-24 12:07:52 UTC (rev 177)
@@ -3,7 +3,7 @@
 
 Begin by starting R. It is recommended that you use the latest version.
 <br /><br />
-Start by enabling all repositories in R so the dependencies of TAPS can be found.<br /><br />
+Enable all repositories in R so the dependencies of TAPS can be found.<br /><br />
 
 <pre>
     setRepositories()
@@ -16,7 +16,7 @@
     install.packages("fields")
 </pre>
 
-To install TAPS enter this command in R.
+Install TAPS.
 
 <br /><br />
 
@@ -24,7 +24,7 @@
     install.packages("TAPS", repos="http://R-Forge.R-project.org")
 </pre>
 
-If for some reason that does not work try installing it from source by adding 'type="source"' to the command.
+If for some reason that does not work, try installing it from source by adding 'type="source"' to the command.
 <pre>
     install.packages("TAPS", repos="http://R-Forge.R-project.org",type="source")
 </pre>