README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# SCNA

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This repository contains all the supplementary files and/or R code to generate all the data used in the article: 
***["Refinement of computational identification of somatic copy number alterations using DNA methylation microarrays illustrated in cancers of unknown primary"]( https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac161/6582004?login=false).***

# cnv.methyl Package:

[cnv.methyl package](https://github.com/ijcBIT/cnv.methyl.git) has been created in order to collect and share all the functions and code used for the pipline. It is written fully in R and you can install the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("https://github.com/ijcBIT/cnv.methyl.git")
```

## Examples:

You can follow the "Manual.Rmd" document with walk-through examples of all the different steps in the pipline.