CNVplot
April 5, 2017 ยท View on GitHub
Plot CNV data with a genome viewer in R.
Installation
Install in R with 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
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.