Description Usage Arguments Details Author(s) See Also
Plots the whole genome coverage vs allelic imbalance with the approximated areas copynumbers and allele constitution. CG_Ka_check is called from the patchwork.CG.copynumbers() function. It would be hard to run this function outside of patchwork.CG.copynumbers().
1 |
chr |
Chromosome. |
start |
Start position of segment. |
end |
End position of segment. |
int |
Ratio between relative coverage and segment length. |
ai |
Allelic imbalance as calculated from (1 - (lesser readcount / greater readcount)) per segment. |
Cn |
Copy number object created in patchwork.CG.copynumbers(). |
mCn |
mCn, object created in patchwork.CG.copynumbers(). |
t |
A list between int and ai. (ratio and allelic imbalance) |
name |
Default is ”. When method is run by patchwork.CG.copynumbers() it will inherit 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. |
Vertical axis: Allelic Imbalance.
Horizontal axis: Relative coverage.
The naming scheme is Copynumber-m-LesserAlleleDistribution So for example 2m0 means copynumber = 2, both allels are the same whereas 2m1 means copynumber = 2, 1 allele each.
Another example: 4m0, copynumber = 4, All allels are the same. (Loss of heterozygosity). 4m1, copynumber = 4, 3 alleles are the same, one is different. 4m2, copynumber = 4, 2 alleles each.
The total number of alleles present are always the copynumber.
Markus Mayrhofer, markus.mayrhofer@medsci.uu.se
Sebastian DiLorenzo, sebastian.dilorenzo@medsci.uu.se
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.