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https://github.com/dantaki/CNVplot
Plot CNV data with a genome viewer in R
https://github.com/dantaki/CNVplot
Last synced: 4 months ago
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Plot CNV data with a genome viewer in R
- Host: GitHub
- URL: https://github.com/dantaki/CNVplot
- Owner: dantaki
- License: mit
- Created: 2016-09-28T02:39:19.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2017-04-05T04:42:09.000Z (about 7 years ago)
- Last Synced: 2024-01-17T00:53:51.995Z (6 months ago)
- Language: R
- Size: 22.5 MB
- Stars: 15
- Watchers: 2
- Forks: 6
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Lists
- awesome-genome-visualization - CNVPlot
- repo-5916-awesome-genome-visualization - CNVPlot - genome-visualization/cnvplot.jpg) (Static)
README
# CNVplot
Plot CNV data with a genome viewer in R.
>[Brandler, W. M., Antaki, D., & Gujral, M. (2015). Frequency and complexity of de novo structural mutation in autism. Am J Hum Genet. doi:10.1101/030270](https://www.ncbi.nlm.nih.gov/pubmed/27018473)
## Installation
Install in R with [devtools](https://github.com/hadley/devtools)
```
install.packages("devtools")
library(devtools)
install_github("dantaki/CNVplot")
```
## Usage
```
CNVplot(df,Start,End,copyNumber,genome,title,yLabel)
```
### Arguments
ARG | Description
--- | ----
df | Input data frame: **See Inputs for formatting requirements**
Start | Start position of the CNV
End | End position of the CNV
copyNumber | Copy number state. Deletion arguments: DEL,del,<2. Duplication arguments: DUP,dup,>2
genome | Reference genome build either hg19 or hg38
title | Title of the plot
yLabel | Y label
## Inputs
* Single individual
CHROM | POSITION | SAMPLE_DATA
--- | --- | ---
chr8 | 1000 | -0.56
chr8 | 1023 | 0.12
* Trio
CHROM | POSITION | PROBAND | MOTHER | FATHER
------| -------- | ------- | ------ | ------
chr8 | 1000 | -0.56 | 0.13 | -0.43
chr8 | 1023 | 0.12 | -0.63 | 0.26
## Author:
* Danny Antaki
* [email protected]
### Acknowledgements:
* William Brandler
* Jonathan Sebat
* Sebat Lab http://sebatlab.ucsd.edu
## License
MIT License
Copyright (c) 2016 Danny Antaki
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.