Description Usage Arguments Details Author(s) See Also
Visualizes the calculated data of patchwork.CG.plot() + patchwork.CG.copynumbers() for each chromosome. See details for a walkthrough of the plot.
1 |
chr |
Chromosomes name of segm object. |
start |
Start position of segment. |
end |
End position of segment. |
int |
Ratio of relative coverage from somaticCnvSegmentsNonDiplod file and segment length. |
ai |
Allelic imbalance. |
Cn |
Copy number. |
mCn |
mCn. |
mchr |
Chromosomes name of depcov (depthOfCoverage file). |
mpos |
Start position from depcov. |
mval |
Ratio between averagenormalizedcoverage and mean(averagenormalizedcoverage) from depthOfCoverage file. |
sval |
Inverse ratio between allele maximum and allele minimum per position. |
schr |
Chromosomes name of mastervar. |
spos |
Start position from mastervar. |
name |
Name that you want output to have. Default is ” which will yield files named as '_KaChCN_chr#.png'. When method is run by patchwork.CG.copynumbers() it will that functions name parameter. |
xlim |
Default is c(0,2.4). Limit of x axis. |
ylim |
Default is c(0,1). Limit of y axis. |
maxCn |
Default is 8. The highest copynumber of the sample to check for. |
Walkthrough of the plot:
TOP
Vertical axis: Allelic Imbalance
Horizontal axis: Total Intensity
The chromosome plotted against the complete genome background. The separation between clusters within the plot are due to the fluctuating intensity and allelic imbalance and as such display the varying allele counts and copy numbers. Longer/larger segments have bigger circles. Darker circles show more content as they are ontop of eachother.
TOP MIDDLE
Vertical axis: Copynumber
Horizontal axis: Chromosomal coordinate
Displays the total and minor copynumbers for different segments of the chromosome in question.
LOWER MIDDLE
Vertical axis: Total Intensity
Horizontal axis: Chromosomal coordinate
The chromosome in questions total intensity plotted against the position on the chromosome.
BOTTOM
Vertical axis: Allelic Imbalance
Horizontal axis: Chromosomal coordinate
The chromosome in questions allelic imbalance plotted against the position on the chromosome.
Markus Mayrhofer, markus.mayrhofer@medsci.uu.se Sebastian DiLorenzo, sebastian.dilorenzo@medsci.uu.se
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