Description Usage Arguments Details Author(s) Examples
Reads files and performs calculations later used in the plotting functions.
In details there is some very important information, highly recommended!
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path |
Path to the ASM folder. One of the subfolders of your completegenomics directory. Should be given as a string. Ex. path="path/to/ASM". |
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. |
Before execution make sure that you have unpacked the necessary files. masterVarBeta, located in your ASM/ folder,somaticCnvSegmentsNonDiploidBeta, located in your ASM/CNV/ folder, and depthOfCoverage, also located in your ASM/CNV/ folder.
If you wish to use this function in a script so it performs its function on multiple genome entries, remember to also loop over the "name" parameter or you run the risk of the plots replacing eachother. The easiest way to script this to run over multiple files is to use the masterVarBeta, somaticCnvSegments and depthOfCoverage parameters as opposed to the path parameter.
It is prudent not do run multiple instances of patchwork.CG.plot in the same directory. This can cause issues with the generated file, read below, and also with plot names if you have kept the default value.
During execution of patchwork.CG.plot a file named CG.Rdata will be built then saved in your working directory. This file is used for plotting purposes in patchwork.CG.copynumbers(). As such, patchwork.CG.copynumbers() should either be executed in the same working directory as this file is located or using the CGfile parameter of patchwork.CG.copynumbers().
Markus Mayrhofer, markus.mayrhofer@medsci.uu.se
Sebastian DiLorenzo, sebastian.dilorenzo@medsci.uu.se
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | ## Not run:
#Load patchworkCG
>library(patchworkCG)
#An example of running patchwork.CG.plot. Note that the path is to the ASM folder
#of the default CompleteGenomics File structure.
>patchwork.CG.plot(path="Data/HCC2218/GS00258-DNA_B03/GS00258-DNA_B03/ASM",
name="HCC2218_")
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
#The values used to generate the plots are saved in three objects,
#mastervar,segs and depcov, and can be viewed loading CG.Rdata.
>load("CG.Rdata")
> head(mastervar)
chr begin end vartype ref_count tot_count ref_countN tot_countN
876 chr1 46669 46670 snp 1 1 2 3
912 chr1 49313 49315 sub 69 129 71 123
1030 chr1 55387 55388 snp 64 211 78 247
1042 chr1 55815 55816 snp 5 12 3 10
1054 chr1 56484 56485 snp 0 11 2 6
1082 chr1 57989 57990 snp 58 187 56 177
mut_count max min ratio
876 0 1 0 0.01635786
912 60 69 60 2.11016381
1030 147 147 64 3.45150825
1042 7 7 5 0.19629431
1054 11 11 0 0.17993645
1082 129 129 58 3.05891963
> head(segs)
chr start end avgnormcov relcov ratio snvs ai
1 chr1 10000 177417 88.2 1.36 1.0434479 42 0.5449591
2 chr1 227417 267719 88.2 1.36 1.0434479 0 0.0000000
3 chr1 317719 471368 88.2 1.36 1.0434479 2 1.0000000
4 chr1 521368 600000 61.4 0.95 0.8015226 1 1.0000000
5 chr1 600000 2634220 93.9 1.45 1.0965535 895 0.6904948
6 chr1 2684220 3845268 93.9 1.45 1.0965535 570 0.8107859
> head(depcov)
chr begin end avgnormcov ratio
1 chr1 10000 100000 94.8 1.0897044
2 chr1 100000 177417 102.9 1.1622234
3 chr1 227417 267719 124.4 1.3547120
4 chr1 317719 400000 99.5 1.1317833
5 chr1 400000 471368 83.9 0.9921172
6 chr1 521368 600000 70.1 0.8685663
## End(Not run)
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