[Patchwork-commits] r133 - www

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

Author: sebastian_d
Date: 2012-06-04 15:17:56 +0200 (Mon, 04 Jun 2012)
New Revision: 133

Modified:
   www/pw_exec.php
Log:
Updated uniform parameter names for patchwork.plot

Modified: www/pw_exec.php
===================================================================
--- www/pw_exec.php	2012-05-08 13:14:40 UTC (rev 132)
+++ www/pw_exec.php	2012-06-04 13:17:56 UTC (rev 133)
@@ -33,19 +33,19 @@
 <pre>
 	Usage:
 
-	     patchwork.plot(BamFile,Pileup,reference=NULL,normal.bam=NULL,normal.pileup=NULLAlpha=0.0001,SD=1)
+	     patchwork.plot(BamFile,Pileup,Reference=NULL,Normal.bam=NULL,Normal.pileup=NULL,Alpha=0.0001,SD=1)
 	     
 	Arguments:
 
 	 BamFile: Aligned, Sorted Bam-file.
 	  Pileup: Pileup file generated through samtools -vcf reference.fasta
 	          bamfile > outfile.
-	reference: Default is NULL.  Path to a reference file that can be
+	Reference: Default is NULL.  Path to a reference file that can be
 	          created using patchwork.createreference() or downloaded from
 	          patchworks homepage.
-	normal.bam: Default is NULL.  The matched normal sample of the your
+	Normal.bam: Default is NULL.  The matched normal sample of the your
 	          BamFile.
-	normal.pileup: Default is NULL.  The pileup of your normal sample.
+	Normal.pileup: Default is NULL.  The pileup of your normal sample.
 	   Alpha: Default 0.0001, change if you want to try to get a better
 	          segmentation from patchwork.segment().  From DNAcopy
 	          (?segment): alpha: significance levels for the test to accept
@@ -60,7 +60,7 @@
 Example run of patchwork.plot() where output has been left for display: <br />
 
 <pre style="height:200px;overflow:scroll;">
-	patchwork.plot(BamFile="patchwork.example.bam",Pileup="patchwork.example.pileup",reference="../HCC1954/datasolexa.RData")
+	patchwork.plot(BamFile="patchwork.example.bam",Pileup="patchwork.example.pileup",Reference="../HCC1954/datasolexa.RData")
 		Initiating Allele Data Generation
 		Initiating Read Chromosomal Coverage 
 		Reading chr1