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Expand Up @@ -18,7 +18,7 @@ Please make sure to check our other projects at [loosolab](http://loosolab.mpi-b

#### Input

As input all data can be used, which show a multimodel distribution. The package was first tested with mRNA data from TCGA (s. example).
As input all data can be used, which show a multimodel distribution. The package was first tested with mRNA data from TCGA.
A standardized format was needed to allow the formation of a connection between the multimodality recognition and the pathway analyses. This JavaScript Object Notation (JSON) contains each gene with its number of modalities and the connected means, standard deviation, sizes and the belonging patients in the parameter “groups”. Also, the location of the files that contain clinical data and the expression matrix should be given. An example of the needed data format is given in Table 1.

![Table1](./PARrOT/vignettes/table1.PNG "Table 1")
Expand All @@ -45,21 +45,23 @@ This can be loaded into R and prepared for a second anaylsis run where all infor
readcluster(clustermember = block_member.csv, matrix = matrix)
````

This generates a file for each found cluster named like subcluster_<number of cluster>.txt. It includes the information
By this a file for each found cluster is generated. Naming the files as follows: subcluster_<number of cluster>.txt.
This files contain all edges and all modalties for a found cluster of the first run of Graph analyses.

````bash
python ./Graph_subcluster.py -i <OUTPUT dir> -o <your OUTPUT dir>
````
This performs a whole analysis for each cluster.

## docker
## Docker

The whole analysis can also be performed with the help of the dockker container.
It can easily started by this command.

````bash
docker run -i -v <dir containing JSON>:/INPUT/ -v <desired OUTPUT dir>:/OUTPUT/ parrot:latest
````

In the input directory only one json file is suposed to be located and the output directory is supposed to be empty.
The Docker container can be obtained [here](https://cloud.docker.com/u/loosolab/repository/docker/loosolab/parrot).

Expand Down Expand Up @@ -123,6 +125,7 @@ The functionality has been tested with a randomised data pool. Into this data po
## Installation

To install the R-package the following commands have to be executed in R.

```r
library(devtools)
install_github(repo = "loosolab/PARrOT/PARrOT",host = "github.molgen.mpg.de/api/v3")
Expand Down