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Fix links in README (#100)
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@yunhailuo
yunhailuo authored Aug 24, 2019
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Expand Up @@ -210,7 +210,7 @@ Advanced usage with XenaDataset and its subclasses
- **Build GDC importing pipelines with** ``GDCOmicset``, ``GDCPhenoset`` **or** ``GDCSurvivalset`` **classes**
``GDCOmicset``, ``GDCPhenoset`` and ``GDCSurvivalset`` are subclasses of ``XenaDataset`` and are preloaded with settings for importing GDC genomic data, TCGA phenotype data on GDC, TARGET phenotype data on GDC and GDC's survival data respecitively. These settings can be customized by setting corresponding properties described below. For more details, please check the `next section <#gdc-etl-settings>`__ and the `documentation <docs/API.rst>`_.
``GDCOmicset``, ``GDCPhenoset`` and ``GDCSurvivalset`` are subclasses of ``XenaDataset`` and are preloaded with settings for importing GDC genomic data, TCGA phenotype data on GDC, TARGET phenotype data on GDC and GDC's survival data respecitively. These settings can be customized by setting corresponding properties described below. For more details, please check the `next section <#gdc-etl-settings>`__ and the `documentation <https://github.com/ucscXena/xena-GDC-ETL/blob/master/docs/API.rst>`_.
The script for ``gdc2xena.py`` command line is a good example for basic usage of these classes. Similar to ``XenaDataset``, a GDC dataset is defined by ``projects``, which is one or a list of valid GDC "project_id". For ``GDCOmicset``, a dataset should also be defined with one of the supported ``xena_dtype`` (find out with the class method ``GDCOmicset.get_supported_dtype()``). The ``xena_dtype`` is critical for a ``GDCOmicset`` object selecting correct default settings. For ``GDCPhenoset`` and ``GDCSurvivalset``, data type are self-explanatory and cannot be changed. Therefore, you can instantiate these classes like this:
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+-------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| raws2matrix | Used by the ``transform`` method and responsible for both merging multiple GDC raw data into one Xena matrix and processing new Xena matrix as needed. | ``callable``: takes only 1 list of ``read_raw`` returns as its argument and returns an object (usually a pandas DataFrame) which has a ``to_csv`` method for saving as a file. | Check `GDC genomic transform settings`_ for details |
+-------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| metadata_template | Used by the ``metadata`` method for rendering metadata by Jinja2. | ``jinja2.environment.Template`` or ``str``: a ``jinja2.environment.Template`` used directly by Jinja2; if it's a string, it is a path to the template file which will be silently read and converted to ``jinja2.environment.Template``. | `Resources <Resources>`_ |
| metadata_template | Used by the ``metadata`` method for rendering metadata by Jinja2. | ``jinja2.environment.Template`` or ``str``: a ``jinja2.environment.Template`` used directly by Jinja2; if it's a string, it is a path to the template file which will be silently read and converted to ``jinja2.environment.Template``. | `Resources <https://github.com/ucscXena/xena-GDC-ETL/blob/master/Resources>`_ |
+-------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| metadata_vars | Used by the ``metadata`` method for rendering metadata by Jinja2. | ``dict``: used directly by Jinja2 which should match variables in ``metadata_template``. | :: |
| | | | |
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Documentation
-------------
Check documentation for GDC module and Xena Dataset module `here <docs/API.rst>`_.
Check documentation for GDC module and Xena Dataset module `here <https://github.com/ucscXena/xena-GDC-ETL/blob/master/docs/API.rst>`_.

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