Merge pull request #33 from adeschen/master

Adding citing section to README and vignette

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CNVMetrics
 Type: Package
-Version: 0.1.5
+Version: 0.1.6
 Date: 2021-02-17
 Title: Copy Number Variant Metrics
 Description: The CNVMetrics package calculates similarity metrics to 

NEWS.md

@@ -1,9 +1,22 @@
+# CNVMetrics 0.1.6
+
+NEW FEATURES
+
+* `calculateLog2ratioMetric()` method enables log2 ratio metric calculation using similar workflow than `calculateOverlapRegionsMetric()` method.
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+* `plotMetric()` replaces `plotOverlapMetric()` method. The new method can plot all metrics (state call metrics and log2 ratio metrics).
+* Vignette section 'Workflow for metrics calculated using the level of amplification/deletion' is complete.
+* New citing section in README and vignette refering to published F1000Research poster (http://www.doi.org/10.7490/f1000research.1118704.1). 
+* Instead of calculating distance, log2 ratio metrics are calculated distance-based metrics (1/(1+distance)).
+
 # CNVMetrics 0.1.4
 
 SIGNIFICANT USER-VISIBLE CHANGES
 
 * New website https://krasnitzlab.github.io/CNVMetrics/index.html associated to package.
-* Vignette section 'Workflow for metrics calculated using CNV status calls' is completed.
+* Vignette section 'Workflow for metrics calculated using CNV status calls' is complete.
 
 # CNVMetrics 0.1.3
 

README.md

@@ -12,27 +12,29 @@ The **_CNVMetrics_** package offers multiple quantitative metrics of similarity
 Among these are metrics based on CNV status calls only (amplification/deletion status) or on the level of amplification/deletion. In addition, a visualization tool is provided to explore resulting metrics.
 
 
+## Citing ## 
+
+If you use this package for a publication, we would ask you to cite the following:
+
+>Belleau P, Deschênes A, Beyaz S et al. CNVMetrics package: Quantifying similarity between copy number profiles [version 1; not peer reviewed]. F1000Research 2021, 10:737 (slides) (doi: 10.7490/f1000research.1118704.1)
+
+[F1000Research poster](http://www.doi.org/10.7490/f1000research.1118704.1)
+
+
 ## Authors ##
 
 [Astrid Deschênes](http://ca.linkedin.com/in/astriddeschenes "Astrid Deschênes"),
 [Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau "Pascal Belleau") and 
 [Alexander Krasnitz](https://www.cshl.edu/research/faculty-staff/alexander-krasnitz/ "Alexander Krasnitz")
 
 
-## License ##
-
-This package and the underlying **_CNVMetrics_** code are distributed under 
-the Artistic license 2.0. You are free to use and redistribute this software. 
-
-For more information on Artistic 2.0 License see
-[http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0)
-
 ## Documentation ##
 
 [CNVMetrics Website](https://krasnitzlab.github.io/CNVMetrics/)
 
 [CNVMetrics Get Started](https://krasnitzlab.github.io/CNVMetrics/articles/CNVMetrics.html)
 
+
 ## Installation ##
 
 To install the latest version accessible, the  [devtools](https://cran.r-project.org/web/packages/devtools/index.html) 
@@ -44,6 +46,16 @@ package is required.
      ## Install the latest version of CNVMetrics
      devtools::install_github('KrasnitzLab/CNVMetrics')
 
+
+## License ##
+
+This package and the underlying **_CNVMetrics_** code are distributed under 
+the Artistic license 2.0. You are free to use and redistribute this software. 
+
+For more information on Artistic 2.0 License see
+[http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0)
+
+
 ## Bugs/Feature requests ##
 
 If you have any bugs or feature requests, 

vignettes/CNVMetrics.Rmd

@@ -35,16 +35,22 @@ set.seed(121444)
 **License**: `r packageDescription("CNVMetrics")[["License"]]`<br />
 
 
-<br>
-<br>
-
 # Licensing 
 
 The `r Githubpkg("KrasnitzLab/CNVMetrics")` package and the underlying 
 `r Githubpkg("KrasnitzLab/CNVMetrics")` code are distributed under the 
 Artistic license 2.0. You are free to use and redistribute this software. 
 
 
+<br>
+<br>
+
+# Citing
+
+If you use this package for a publication, we would ask you to cite the following:
+
+>Belleau P, Deschênes A, Beyaz S et al. CNVMetrics package: Quantifying similarity between copy number profiles [version 1; not peer reviewed]. F1000Research 2021, 10:737 (slides) (doi: 10.7490/f1000research.1118704.1)
+
 <br>
 <br>