Description Usage Arguments Details Author(s) See Also
Visualises the calculated data of patchwork.plot() + patchwork.copynumbers() for each chromosome. See details for a walkthrough of the plot.
1 |
chr |
Chromosomes name of segs object. Final version of segs created from patchwork.Medians_n_AI(). |
start |
Start position of segment. |
end |
End position of segment. |
int |
Normalized coverage. |
ai |
Allelic imbalance. |
Cn |
Copy number. |
mCn |
mCn. |
mchr |
Chromosomes name of kbsegs object. Final version of kbsegs created from patchwork.smoothing(). |
mpos |
Middle position of kbsegs segments. |
mval |
Ratio between kbsegs coverage and refcoverage. |
schr |
Chromosome names of alf object. Final version of alf created from patchwork.alleledata(). |
spos |
Positions in alf. |
sval |
Inverse ratio between allele maximum and allele minimum. |
t |
A list of approximate copynumber and allelic imbalance positions. |
name |
Name of sample. patchwork.plot sends it as name of the bamfile. |
parameters |
The parameters sent to patchwork.copynumbers() to be plotted. |
xlim |
Default is c(0,2.5). Limit of x axis. |
ylim |
Default is 0:1. Limit of y axis. |
maxCn |
Default is 8. The highest copynumber of the sample to check for. |
Walkthrough of the plot:
LEFT
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 RIGHT
Vertical axis: Copynumber
Horizontal axis: Chromosomal coordinate
Displays the total and minor copynumbers for different segments of the chromosome in question.
UPPER MIDDLE RIGHT
Vertical axis: Total Intensity
Horizontal axis: Chromosomal coordinate
The chromosome in questions total intensity plotted against the position on the chromosome.
LOWER MIDDLE RIGHT
Cytoband information.
BOTTOM RIGHT
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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