germline_filter: Plot expected germline and somatic VAF along with observed...
In AxelitoMartin/TumorEvolution:
View source: R/germline_filter.R
Description
Plot expected germline and somatic VAF along with observed somatic VAF.
And retrieve the the mutational status infered by the method.
Variants found to have an observed VAF below 2 standard deviations below the expected value are considered "subclonal".
Those falling in the +/- 2 standard deviation range from the expected VAF are annoatated "neutral".
Those with VAF greater than 2 starndard deviation above the expected value are annotated as "artifacts".
Usage
1
germline_filter(mat, purity, alpha = 0.05, plot = TRUE, sample)
Value
mat.out
AxelitoMartin/TumorEvolution documentation built on Jan. 12, 2021, 2:43 a.m.
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View source: R/germline_filter.R
Description
Plot expected germline and somatic VAF along with observed somatic VAF. And retrieve the the mutational status infered by the method. Variants found to have an observed VAF below 2 standard deviations below the expected value are considered "subclonal". Those falling in the +/- 2 standard deviation range from the expected VAF are annoatated "neutral". Those with VAF greater than 2 starndard deviation above the expected value are annotated as "artifacts".
Usage
1 | germline_filter(mat, purity, alpha = 0.05, plot = TRUE, sample)
|
Value
mat.out
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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