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# superFreq RNA paper
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A public repo to reproduce the plots in the paper "Detecting copy number alterations in RNA-Seq using SuperFreq".
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# How to run

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Download the repo, open R and
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```
source('compareMethods.R')
```
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You need superFreq and vioplot R-packages installed. It is tested on R v3.6.0.
SuperFreq can be installed from [https://github.com/ChristofferFlensburg/superFreq](https://github.com/ChristofferFlensburg/superFreq).
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SuperFreq can be installed with
```
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()
BiocManager::install("GenomeInfoDb")
BiocManager::install("GenomicFeatures")
BiocManager::install("VariantAnnotation")
install.packages("devtools")
library(devtools)
install_github('ChristofferFlensburg/superFreq')
```

vioplot can be installed with
```
install.packages("vioplot")
```

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# Expected output
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The script takes about 5 minutes to run, and should produce the plots and supplementary plots in a new directory. It should match the already present expectedPlots directory.