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find_redundant_contigs
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====================== ===============
find_redundant_contigs R Documentation
====================== ===============

Find redundant contigs within a bin
-----------------------------------

Description
~~~~~~~~~~~

Find contigs with overlapping marker genes in a given bin, and suggest
contigs to be removed in order to reduce contamination without affecting
completeness. Note that this can give a quick idea of the contigs that
are sources of contamination within a bin, but is not a replacement for
proper bin refininement with other tools such as anvi\\'o.

Usage
~~~~~

.. code:: R

   find_redundant_contigs(SQM, bin, minimum_overlap_for_removal = 1)

Arguments
~~~~~~~~~

+---------------------------------+------------------------------------+
| ``SQM``                         | A SQM object.                      |
+---------------------------------+------------------------------------+
| ``bin``                         | character. Name of the bin to be   |
|                                 | created.                           |
+---------------------------------+------------------------------------+
| ``minimum_overlap_for_removal`` | numeric. Fraction of marker genes  |
|                                 | in the contigs present in another  |
|                                 | contig needed to suggest it for    |
|                                 | removal. If set to ``1``           |
|                                 | (default), contigs will only       |
|                                 | suggested for removal if their     |
|                                 | markers fully overlap with those   |
|                                 | in another contig (and thus        |
|                                 | completeness will not change after |
|                                 | removing them). Smaller values     |
|                                 | will result in more contigs being  |
|                                 | suggested for removal, which will  |
|                                 | further reduce contamination at    |
|                                 | the expense of some completeness.  |
+---------------------------------+------------------------------------+

Value
~~~~~

A character vector with the contigs deemed to be redundant. A heatmap
showing how marker genes overlap over different contigs will also be
produced.

See Also
~~~~~~~~

``create_bin``, ``remove_contigs_from_bin``

Examples
~~~~~~~~

.. code:: R

   data(Hadza)
   bin_name = "Hadza2merged.concoct.28.fa.contigs"
   # Get redundant contigs that could be removed from our bin
   candidates_for_removal = find_redundant_contigs(Hadza, bin_name)
   # We can now remove them from the bin
   Hadza.new.1 = remove_contigs_from_bin(Hadza, bin_name, candidates_for_removal)
   # Or we can create a new bin out of them
   #  which will also remove them from the original bin
   Hadza.new.2 = create_bin(Hadza, "new_bin_name", candidates_for_removal)