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Merge pull request #34 from vyepez88/documentation
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q dim added as parameter
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vyepez88 committed Apr 17, 2020
2 parents 9ae6722 + c9273ec commit 1b806e3
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63 changes: 36 additions & 27 deletions docs/source/prepare.rst
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Expand Up @@ -61,36 +61,38 @@ tools dictionary A key-value list of different commands (key) an
Aberrant expression dictionary
++++++++++++++++++++++++++++++

================ ========= ===================================================================================================================================== ======
Parameter Type Description Default/Examples
================ ========= ===================================================================================================================================== ======
groups list DROP groups that should be executed in this module. If not specified or ``null`` all groups are used. ``- group1``

``- group2``
minIds numeric A non-negative number indicating the minimum number of samples that a group needs in order to be analyzed. We recommend at least 50. ``1``
fpkmCutoff numeric A non-negative number indicating the minimum FPKM 5% of the samples per gene should have. If a gene has less it will be filtered out. ``1 # suggested by OUTRIDER``
implementation character Either 'autoencoder', 'pca' or 'peer'. Methods to remove sample covariation in OUTRIDER. ``autoencoder``
zScoreCutoff numeric A non-negative number. Z scores (in absolute value) greater than this cutoff are considered as outliers. ``0``
padjCutoff numeric A number between (0, 1] indicating the maximum FDR an event can have in order to be considered an outlier. ``0.05``
================ ========= ===================================================================================================================================== ======
============================ ========= ===================================================================================================================================== ======
Parameter Type Description Default/Examples
============================ ========= ===================================================================================================================================== ======
groups list DROP groups that should be executed in this module. If not specified or ``null`` all groups are used. ``- group1``

``- group2``
minIds numeric A non-negative number indicating the minimum number of samples that a group needs in order to be analyzed. We recommend at least 50. ``1``
fpkmCutoff numeric A non-negative number indicating the minimum FPKM 5% of the samples per gene should have. If a gene has less it will be filtered out. ``1 # suggested by OUTRIDER``
implementation character Either 'autoencoder', 'pca' or 'peer'. Methods to remove sample covariation in OUTRIDER. ``autoencoder``
zScoreCutoff numeric A non-negative number. Z scores (in absolute value) greater than this cutoff are considered as outliers. ``0``
padjCutoff numeric A number between (0, 1] indicating the maximum FDR an event can have in order to be considered an outlier. ``0.05``
maxTestedDimensionProportion numeric An integer that controls the maximum value that the encoding dimension can take. Refer to the advanced options below. ``3``
============================ ========= ===================================================================================================================================== ======

Aberrant splicing dictionary
++++++++++++++++++++++++++++

======================== ========= ============================================================================================ ======
Parameter Type Description Default/Examples
======================== ========= ============================================================================================ ======
groups list Same as in aberrant expression. ``# see aberrant expression example``
minIds numeric Same as in aberrant expression. ``1``
recount boolean If true, it forces samples to be recounted. ``false``
longRead boolean Set to true only if counting Nanopore or PacBio long reads. ``false``
filter boolean If false, no filter is applied. We recommend filtering. ``true``
minExpressionInOneSample numeric The minimal read count in at least one sample required for an intron to pass the filter. ``20``
minDeltaPsi numeric The minimal variation (in delta psi) required for an intron to pass the filter. ``0.05``
implementation character Either 'PCA' or 'PCA-BB-Decoder'. Methods to remove sample covariation in FRASER. ``PCA``
deltaPsiCutoff numeric A non-negative number. Delta psi values greater than this cutoff are considered as outliers. ``0.3 # suggested by FRASER``
padjCutoff numeric Same as in aberrant expression. ``0.1``
======================== ========= ============================================================================================ ======
============================ ========= ============================================================================================ ======
Parameter Type Description Default/Examples
============================ ========= ============================================================================================ ======
groups list Same as in aberrant expression. ``# see aberrant expression example``
minIds numeric Same as in aberrant expression. ``1``
recount boolean If true, it forces samples to be recounted. ``false``
longRead boolean Set to true only if counting Nanopore or PacBio long reads. ``false``
filter boolean If false, no filter is applied. We recommend filtering. ``true``
minExpressionInOneSample numeric The minimal read count in at least one sample required for an intron to pass the filter. ``20``
minDeltaPsi numeric The minimal variation (in delta psi) required for an intron to pass the filter. ``0.05``
implementation character Either 'PCA' or 'PCA-BB-Decoder'. Methods to remove sample covariation in FRASER. ``PCA``
deltaPsiCutoff numeric A non-negative number. Delta psi values greater than this cutoff are considered as outliers. ``0.3 # suggested by FRASER``
padjCutoff numeric Same as in aberrant expression. ``0.1``
maxTestedDimensionProportion numeric Same as in aberrant expression. ``6``
============================ ========= ============================================================================================ ======


Mono-allelic expression dictionary
Expand Down Expand Up @@ -155,8 +157,15 @@ them. For example, to add new plots to the ``Summary`` scripts, or add
columns to the results tables. Also, users might want to modify the threads of
each script. Finally, other functionalities can be added.

The aberrant expression and splicing modules use a denoising autoencoder to
correct for sample covariation. This process reduces the fitting space to a
dimension smaller than the number of samples N. The encoding dimension is optimized.
We recommend the search space to be at most N/3 for the aberrant expression,
and N/6 for the aberrant splicing case. Nevertheless, the user can specify the
denominator with the parameter ``maxTestedDimensionProportion``.

In order to influence which fields of the BAM files are imported, the user can
provide a `scanBamParam` object. This will affect how the files are counted in
provide a ``scanBamParam`` object. This will affect how the files are counted in
the aberrant expression and splicing modules. Refer to the function's
`documentation <https://www.rdocumentation.org/packages/Rsamtools/versions/1.24.0/topics/ScanBamParam>`_ for details.

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