[Patchwork-commits] r103 - in pkg/patchwork: . R man

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

Author: sebastian_d
Date: 2012-02-27 13:54:13 +0100 (Mon, 27 Feb 2012)
New Revision: 103

Modified:
   pkg/patchwork/R/zzz.R
   pkg/patchwork/README
   pkg/patchwork/man/patchwork.CNA.Rd
Log:
commit

Modified: pkg/patchwork/R/zzz.R
===================================================================
--- pkg/patchwork/R/zzz.R	2012-02-20 15:30:07 UTC (rev 102)
+++ pkg/patchwork/R/zzz.R	2012-02-27 12:54:13 UTC (rev 103)
@@ -5,4 +5,4 @@
 	cite us! \n 
 	How to run this \n"
 	)
-	}
\ No newline at end of file
+	}

Modified: pkg/patchwork/README
===================================================================
--- pkg/patchwork/README	2012-02-20 15:30:07 UTC (rev 102)
+++ pkg/patchwork/README	2012-02-27 12:54:13 UTC (rev 103)
@@ -7,6 +7,7 @@
 /-------------------/
 
 #Start R (as of writing version 2.14.0)
+
     source("http://bioconductor.org/biocLite.R")
     biocLite("DNAcopy")
 
@@ -15,14 +16,60 @@
     install.packages("patchworkData", repos="http://R-Forge.R-project.org")
     install.packages("patchwork", repos="http://R-Forge.R-project.org")
 
-#If for some reason that does not work, it happened to me, add the type=source to it, as so:
+#If for some reason that does not work add the 'type="source"' to it, as so:
 
     install.packages("patchworkData", repos="http://R-Forge.R-project.org",type="source")
     install.packages("patchwork", repos="http://R-Forge.R-project.org",type="source")
 
-Good luck! =)
 
+/-------------------/
+	Tutorial:
+/-------------------/
 
+	/-------------------/
+		Requirements:
+	/-------------------/
+
+Your samples BAM and BAI file:
+	To get BAI run "samtools index <yourfile>.bam"
+
+A Pileup of your sample created with the 0.1.18 or older version of samtools.
+	"samtools pileup -vcf <reference.fasta> <yourfile>.bam > <yourpileup>"
+
+Either a normal.bam and normal.pileup or a reference file. More on this later.
+
+A working R installation.
+
+
+	/-------------------/
+		Execution:
+	/-------------------/
+
+It is recommended that you run patchwork from a "clean" working directory. In this way you do not run the risk of having files write over eachother. If you do not want to type paths into R you may also want to put the required files in this folder.
+
+Text with a ">" infront is R code.
+
+> library(patchwork)
+> library(patchworkData)
+> patchwork.CNA(BamFile="patchwork.example.bam",Pileup="patchwork.example.pileup",reference="../HCC1954/datasolexa.RData")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Execution may take quite a while depending on the size of your sample! So if possible run it on a dedicated computer.
+
 /------------------------------------/
 Contact information:
 Sebastian.Dilorenzo at medsci.uu.se

Modified: pkg/patchwork/man/patchwork.CNA.Rd
===================================================================
--- pkg/patchwork/man/patchwork.CNA.Rd	2012-02-20 15:30:07 UTC (rev 102)
+++ pkg/patchwork/man/patchwork.CNA.Rd	2012-02-27 12:54:13 UTC (rev 103)
@@ -13,10 +13,13 @@
 
 For now the package is only able to run on unix based systems since it uses
 several system commands when executing such as cp and rm.
+
+\bold{You should use either the reference parameter OR the normal.bam and normal.pileup parameters.}
+
 }
 
 \usage{
-patchwork.CNA(BamFile,Pileup,reference,Alpha=0.0001,SD=1)
+patchwork.CNA(BamFile,Pileup,reference=NULL,normal.bam=NULL,normal.pileup=NULLAlpha=0.0001,SD=1)
 }
 
 \arguments{
@@ -28,9 +31,17 @@
 	samtools -vcf reference.fasta bamfile > outfile.
 	}
   \item{reference}{
-	Path to a reference file that you have either downloaded from us or created yourself with
-	patchwork.createreference().
+  	Default is NULL.
+	Path to a reference file that can be created using patchwork.createreference().
 	}
+	\item{normal.bam}{
+	Default is NULL.
+	The matched normal sample of the your BamFile.
+	}
+	\item{normal.pileup}{
+	Default is NULL.
+	The pileup of your normal sample.
+	}
 	\item{Alpha}{
 	Default 0.0001, change if you want to try to get a better segmentation from patchwork.segment().
 	From DNAcopy (?segment):
@@ -46,7 +57,7 @@
 \details{
 \bold{Make sure to only run one sample at a time in a single working directory
 as standard file names are created. If you do not heed this warning you
-will end up with a complete mess and probably runtime errors as patchwork.readChroms
+will end up with a complete mess and probably runtime errors as patchwork
 tries to run simultaniously for multiple samples in the same working directory.}
 
 Upon completion of the the method you may receive the following kinds of warnings:
@@ -61,8 +72,7 @@
 
 etc...  
 
-This is not unusal, it just means its the first time you've run the patchwork.CNA
-function in this directory.
+This is not unusal, it just means that it is the first time you've run the patchwork.CNA function in this directory.
 The patchwork function will check if you have data.Rdata or pile.alleles.Rdata etc
 in your working directory to avoid remaking these, should they already exist.