.. _`bio/rubic`:

RUBIC
=====


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/rubic?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/rubic

`RUBIC <http://ccb.nki.nl/software/rubic/doc/>`_
detects recurrent copy number alterations using copy number breaks.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule rubic:
        input:
            seg="{samples}/segments.txt",
            markers="{samples}/markers.txt"
        output:
            out_gains="{samples}/gains.txt",
            out_losses="{samples}/losses.txt",
            out_plots=directory("{samples}/plots") #only possible to provide output directory for plots
        params:
            fdr="",
            genefile=""
        wrapper:
            "v3.0.1/bio/rubic"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``r-base=3.4.1``
* ``r-rubic=1.0.3``
* ``r-data.table=1.10.4``
* ``r-pracma=2.0.4``
* ``r-ggplot2=2.2.1``
* ``r-gtable=0.2.0``
* ``r-codetools=0.2_15``
* ``r-digest=0.6.12``

Input/Output
------------
**Input:**

* seg
* markers

**Output:**

* out_gains
* out_losses
* out_plots



Params
------

* ``fdr``: false discovery rate (optional, leave empty to use default value of 0.25)

* ``genefile``: file path to use custom gene file (optional, leave empty to use default file)




Authors
-------

* Beatrice F. Tan


Code
----

.. code-block:: R

    # __author__ = "Beatrice F. Tan"
    # __copyright__ = "Copyright 2018, Beatrice F. Tan"
    # __email__ = "beatrice.ftan@gmail.com"
    # __license__ = "LUMC"

    library(RUBIC)

    all_genes <- if (snakemake@params[["genefile"]] == "") system.file("extdata", "genes.tsv", package="RUBIC") else snakemake@params[["genefile"]]
    fdr <- if (snakemake@params[["fdr"]] == "") 0.25 else snakemake@params[["fdr"]]

    rbc <- rubic(fdr, snakemake@input[["seg"]], snakemake@input[["markers"]], genes=all_genes)
    rbc$save.focal.gains(snakemake@output[["out_gains"]])
    rbc$save.focal.losses(snakemake@output[["out_losses"]])
    rbc$save.plots(snakemake@output[["out_plots"]])


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