zzz: Welcome to patchworkCG

Description Details Author(s)

Description

PatchworkCG allows you to obtain allele-specific copy number information from Complete Genomics data.

To use patchwork on other data formats,bam and pileups, download patchwork and patchworkData.

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http://patchwork.r-forge.r-project.org/
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It is highly recommended that you visit the webpage for this project as it contains the most recently updated information and instructions regarding everything patchwork.

Details

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Installation Guide: PatchworkCG
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Start the latest version of R.(as of writing 2.14.2)

Text with a ">" infront is R executions.

> install.packages("patchworkCG", repos="http://R-Forge.R-project.org")

If for some reason that does not work add the 'type="source"' to it, as so:

> install.packages("patchworkCG", repos="http://R-Forge.R-project.org",type="source")

The source codes can also be downloaded outside of R at https://r-forge.r-project.org/R/?group_id=1250

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Tutorial:
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Requirements:
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An unpacked CompleteGenomics tumor genome data ASM directory. Specifically the files ASM/masterVarBeta, CNV/depthOfCoverage and CNV/somaticCnvSegmentsNondiploidBeta.

Some helpful commands for unpacking your CompleteGenomics data (UNIX):
To unpack .tar files:tar -zxvf filename.tar
To unpack .bz2 files:bunzip2 filename.bz2

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Execution: patchwork.CG.plot()
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Start R in your working directory. (Or use setwd() after starting R wherever you choose)

> library(patchworkCG)

See

> ?patchwork.CG.plot

Excerpt from ?patchwork.CG.plot:

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Usage:

patchwork.CG.plot(path=NULL,name='CG_sample',manual_file_input=FALSE, masterVarBeta=NULL,somaticCnvSegments=NULL, depthOfCoverage=NULL)

Arguments:

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 the plots that will be generated.

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.

masterVarBeta: 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.

somaticCnvSegments: 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.

depthOfCoverage: 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. ////////////////////////////////////////////

Probably the easiest way of running patchwork.CG.plot is pointing to the ASM folder:

> patchwork.CG.plot(path="path/to/ASM/")
Reading files from ASM folder
File input complete
Performing calculations
Calculations complete
Saving objects to CG.Rdata
Initiating Plotting
Plotting Complete
patchwork.CG.plot Complete
Please read documentation on running patchwork.CG.copynumbers

Once it is complete there should be several plots in your working directory as well as the file "CG.Rdata".

Execution should take no longer half an hour.

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Execution: patchwork.CG.copynumbers()
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For this function to work you will need to have obtained the CG.Rdata file from patchwork.CG.plot(). If it is located in your working directory you will not need to point to it, otherwise you can input it with the argument "CGfile".

See

> ?patchwork.CG.copynumbers

Excerpt from ?patchwork.CG.copynumbers:

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Usage:

patchwork.CG.copynumbers(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_", CGfile=NULL,forcedelta=F)

Arguments:

cn2: The approximate position of copy number 2, diploid, on total intensity axis.

delta: The difference in total intensity between consecutive copy numbers. For example 1 and 2 or 2 and 3. If copy number 2 has total intensity ~0.6 and copy number 3 har total intensity ~0.8 then delta would be 0.2.

het: Allelic imbalance ratio of heterozygous copy number 2.

hom: Allelic imbalance ratio of Loss-of-Heterozygosity copy number 2.

maxCn: Highest copy number to calculate for. Default is 8.

ceiling: Default is 1.

name: Default is "copynumbers_". The name you want attached to generated plots.

CGfile: Default is NULL. If your CG.Rdata file is not in your working directory, and you dont wish to move it to your working directory, you can simply input the path here as CGfile = "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")

This should have generated several plots in your working directory.

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Interpreting plots
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It is recommended that you visit our project homepage for guidance in interpreting the plots you have generated using patchworkCG.

http://patchwork.r-forge.r-project.org/

Other aids in this is the documentation

>?CG_Ka_check
>?CG_KaCh
>?CG_KaChCN
>?CG_karyotype

If you have any questions please feel free to contact us and we will help you to the best of our extent!

Author(s)

Sebastian DiLorenzo, sebastian.dilorenzo@medsci.uu.se
Markus Mayrhofer, markus.mayrhofer@medsci.uu.se


patchworkCG documentation built on May 2, 2019, 6:47 p.m.

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