[Patchwork-commits] r112 - in pkg: patchwork patchwork/man patchworkCG patchworkCG/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 20 14:58:48 CET 2012
Author: sebastian_d
Date: 2012-03-20 14:58:47 +0100 (Tue, 20 Mar 2012)
New Revision: 112
Modified:
pkg/patchwork/README
pkg/patchwork/man/patchwork.plot.Rd
pkg/patchworkCG/README
pkg/patchworkCG/man/patchwork.CG.plot.Rd
Log:
general update and sync between working copies
Modified: pkg/patchwork/README
===================================================================
--- pkg/patchwork/README 2012-03-13 09:08:39 UTC (rev 111)
+++ pkg/patchwork/README 2012-03-20 13:58:47 UTC (rev 112)
@@ -68,9 +68,20 @@
chr1 127285 A R 0 3 60 1 g B
-A normal.bam or reference file or optional normal.pileup or all three.
-****TEXT OM REFERENCE FILE PILEUP AND NORMALBAM****
+(optional) A matched normal sample to your tumor in BAM
+(optional) A pileup of your normal sample BAM
+(optional) A standard Reference file. (Illumina/Solexa, SOLiD or your own)
+What we mean by this (optional) tag is that you do not need to have all these
+files. There is really no point in using all of them.
+
+If you have a matched normal sample you should make a pileup of this and use those two arguments.
+
+In some cases it may be better to use the pileup and a reference file.
+
+You can also run patchwork.plot with only a reference file.
+See patchwork.createreference for information about the reference file.
+
A working R installation.
Below are some included heads of example files so you can compare and see that your files are the same format.
@@ -80,8 +91,13 @@
Execution: patchwork.createreference()
/------------------------------------------/
-This function creates a reference for you using a pool of samples of your selection. Choosing these samples you should consider factors such as ........ It is recommended that you use atleast 3 bam files to create your own reference.
+This function creates a reference for you using a pool of samples of your selection. Choosing the samples to use for reference creation you should consider these factors:
+ - They should be sequenced using the same technique
+ - They should be from the same organism
+ - They should be non-tumerous
+It is recommended that you use atleast 3 bam files to create your own reference.
+
Start R
Load the patchwork and patchworkData libraries
@@ -108,6 +124,13 @@
Execution may take quite a while depending on the size of your sample! So if possible run it on a dedicated computer.
+Start R
+
+Load the patchwork and patchworkData libraries
+
+ > library(patchwork)
+ > library(patchworkData)
+
Read the excellent documentation for patchwork.plot()
> ?patchwork.plot
@@ -116,7 +139,7 @@
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:
@@ -253,7 +276,7 @@
Segment data extraction Complete
- Saving information objects needed for patchwork.copynumbers in findCNs.Rdata
+ Saving information objects needed for patchwork.copynumbers in copynumbers.Rdata
Initiating Plotting
@@ -265,7 +288,7 @@
If you did it correctly it should have generated similar output as can be seen above.
Your working directory should now have the plots generated from the function, 1 overhead plot and 24 chromosomal plots.
The working directory should also contain the files
- - findCNs.Rdata
+ - copynumbers.Rdata
- data.Rdata
- pile.alleles
- pile.alleles.Rdata
@@ -337,7 +360,7 @@
Execution: patchwork.copynumbers()
/-----------------------------------/
-The only file you absolutely must have in your working for the next part of execution is findCNs.Rdata.
+The only file you absolutely must have in your working for the next part of execution is copynumbers.Rdata.
Read the outstanding documentation for patchwork.copynumbers()
@@ -350,11 +373,11 @@
Usage:
- patchwork.copynumbers(cn2,delta,het,hom,maxCn=8,ceiling=1)
+ patchwork.copynumbers(cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F)
Arguments:
- name: Default is "findCNs_". First part of output name for plots
+ name: Default is "copynumbers_". First part of output name for plots
generated from patchwork.copynumbers().
cn2: The approximate position of copy number 2,diploid, on total
@@ -374,7 +397,10 @@
ceiling: Default is 1.
+ forcedelta: Default is FALSE. If TRUE the delta value will not be
+ subject to small adjustment changes.
+
On our webpage there will also be a picture accompanying this portion pointing to the argument values should the documentation for the function not be sufficient. (http://patchwork.r-forge.r-project.org/)
>patchwork.copynumbers(name="Example_",cn2=0.8,delta=0.3,het=0.5,hom=0.8)
Modified: pkg/patchwork/man/patchwork.plot.Rd
===================================================================
--- pkg/patchwork/man/patchwork.plot.Rd 2012-03-13 09:08:39 UTC (rev 111)
+++ pkg/patchwork/man/patchwork.plot.Rd 2012-03-20 13:58:47 UTC (rev 112)
@@ -1,4 +1,4 @@
-\name{patchwork.plot}
+ \name{patchwork.plot}
\alias{patchwork}
\alias{patchwork.plot}
@@ -32,7 +32,7 @@
}
\item{reference}{
Default is NULL.
- Path to a reference file that can be created using patchwork.createreference().
+ Path to a reference file that can be created using patchwork.createreference() or downloaded from patchworks homepage.
}
\item{normal.bam}{
Default is NULL.
Modified: pkg/patchworkCG/README
===================================================================
--- pkg/patchworkCG/README 2012-03-13 09:08:39 UTC (rev 111)
+++ pkg/patchworkCG/README 2012-03-20 13:58:47 UTC (rev 112)
@@ -49,16 +49,16 @@
Usage:
- patchwork.CG.plot(path,name='CG_sample_',manual_file_input=FALSE,
+ patchwork.CG.plot(path=NULL,name='CG_sample',manual_file_input=FALSE,
masterVarBeta=NULL,somaticCnvSegments=NULL,
depthOfCoverage=NULL)
Arguments:
- path: Path to the ASM folder. One of the subfolders of your
- completegenomics directory.
+ path: Default is NULL. Path to the ASM folder. One of the subfolders of
+ your completegenomics directory.
- name: Default is 'CG_sample_'. The name you wish associated with
+ name: Default is 'CG_sample'. The name you wish associated with
the plots that will be generated.
manual_file_input: Default is FALSE. If you set it to TRUE you will be
@@ -121,7 +121,7 @@
Usage:
patchwork.CG.copynumbers(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_",
- CGfile=NULL)
+ CGfile=NULL,forcedelta=F)
Arguments:
@@ -151,6 +151,9 @@
"path/to/file/CG.Rdata" so patchwork.CG.copynumbers() can find its
data.
+ forcedelta: Default is FALSE. If TRUE the delta value will be absolute
+ and not subject to adjustments.
+
On our webpage there will also be a picture accompanying this portion pointing to the argument values should the documentation for the function not be sufficient. (http://patchwork.r-forge.r-project.org/)
> patchwork.CG.copynumbers(cn2=0.8, delta=0.3, het=0.2, hom=0.8, name="Example_", CGfile="path/to/CG.Rdata")
Modified: pkg/patchworkCG/man/patchwork.CG.plot.Rd
===================================================================
--- pkg/patchworkCG/man/patchwork.CG.plot.Rd 2012-03-13 09:08:39 UTC (rev 111)
+++ pkg/patchworkCG/man/patchwork.CG.plot.Rd 2012-03-20 13:58:47 UTC (rev 112)
@@ -25,26 +25,26 @@
Path to the ASM folder. One of the subfolders of your completegenomics directory.
}
\item{name}{
- Default is 'CG_sample_'. The name you wish associated with the plots that will be generated.
+ Default is 'CG_sample'. The name you wish associated with the plots that will be generated.
}
\item{manual_file_input}{
Default is FALSE. If you set it to TRUE you will be prompted to provide path and filename for
the masterVarBeta, somaticCnvSegmentsNondiploid and depthOfCoverage file.
}
\item{masterVarBeta}{
- Path to AND COMPLETE name of the masterVarBeta file, should you wish to implement it directly. Useful if you want to run
+ Path to and COMPLETE NAME of the masterVarBeta file, should you wish to implement it directly. Useful if you want to run
the program on multiple samples and wish to create a script going from file to file. This saves you
from having to conserve the CompleteGenomics file structure.
Default is NULL.
}
\item{somaticCnvSegments}{
- Path to AND COMPLETE name of the somaticCnvSegments file, should you wish to implement it directly. Useful if you want to run
+ Path to and COMPLETE NAME of the somaticCnvSegments file, should you wish to implement it directly. Useful if you want to run
the program on multiple samples and wish to create a script going from file to file. This saves you
from having to conserve the CompleteGenomics file structure.
Default is NULL.
}
\item{depthOfCoverage}{
- Path to AND COMPLETE name of the depthOfCoverage file, should you wish to implement it directly. Useful if you want to run
+ Path to and COMPLETE NAME of the depthOfCoverage file, should you wish to implement it directly. Useful if you want to run
the program on multiple samples and wish to create a script going from file to file. This saves you
from having to conserve the CompleteGenomics file structure.
Default is NULL.
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