Merge branch 'master' of github.com:rkimoakbioinformatics/roakvar

README.md

@@ -1,20 +1,32 @@
-## roakvar
+## Roakvar
 
-roakvar is an R wrapper for the Python-based genomic variant analysis platform, OakVar, bringing the full power of genomic variant analysis to the R environment.
+Roakvar is an R wrapper for the Python-based genomic variant analysis platform, OakVar, bringing the full power of genomic variant analysis to the R environment.
 
 ## Installation
 
-You can install the development version of roakvar from https://github.com/rkimoakbioinformatics/roakvar with:
+* R side: Roakvar has been submitted to CRAN. Meanwhile, install with:
 
 ``` r
 # install.packages("devtools")
 devtools::install_github("rkimoakbioinformatics/roakvar")
 ```
 
-As roakvar is a wrapper for OakVar, OakVar should be installed as well. Follow the instruction at https://oakvar.readthedocs.io to install OakVar.
+* Python side: As roakvar is a wrapper for OakVar, OakVar should be installed as well. See the instruction at https://oakvar.readthedocs.io for the details of installing OakVar, but basically:
+
+``` bash
+pip install oakvar
+```
 
 ## Example
 
+Annotate a VCF file with ClinVar and read the result into a data frame:
+
+```r
+ov.module.install(modules=list("clinvar", "pandasreporter")) # install the ClinVar and pandas reporter modules.
+result = ov.run(inputs="input.vcf", annotators="clinvar", reports="pandas") # Do the analysis and get the result into a variable.
+df = result$pandas # Get the data frame.
+```
+
 These are basic examples which show you how to solve common problems:
 
 ``` r
@@ -35,3 +47,4 @@ ov.run(inputs=list("exampleinput"), annotators=list("clinvar"), reports=list("vc
 ov.gui(result="exampleinput.sqlite")
 ```
 
+Roakvar's R functions correspond to OakVar's CLI commands one-to-one. See https://oakvar.readthedocs.io for OakVar CLI commands.