ADD: result.rst: Dataset and simulation topics

docs/index.rst

@@ -15,6 +15,7 @@ Welcome to sideRETRO's documentation!
    usage.rst
    retrocopy.rst
    method.rst
+   result.rst
    authors.rst
 
 * :ref:`search`

docs/meson.build

@@ -5,6 +5,7 @@ doc_sources = files(
   'install.rst',
   'intro.rst',
   'method.rst',
+  'result.rst',
   'retrocopy.rst',
   'usage.rst'
 )

docs/result.rst

@@ -0,0 +1,171 @@
+.. _chap_result:
+
+*******
+Results
+*******
+
+To assess **sideRETRO** performance and accuracy, we made a simulated
+dataset whereupon we could have control of **true** positive and
+negative values.
+
+Dataset
+=======
+
+Our dataset for testing is composed of 5 simulated human whole-genome
+sequencing with 40x of depth and 10 randomly distributed retrocopies
+each. In total, we had a list of 30 retrocopies consisting of the last
+1000 bases of the largest transcript of the parental gene. All retrocopies
+was stochastically designed for chromosome, position, strand and zygosity.
+
+.. table:: 30 parental gene names chosen for the simulation
+   :widths: auto
+
+   +--------+--------+-------+---------+-------+
+   | ACAP3  | AMY2B  | ATM   | BCL2    | BRAF  |
+   +--------+--------+-------+---------+-------+
+   | BRCA1  | BRIP1  | DVL1  | FANCD2  | FAT1  |
+   +--------+--------+-------+---------+-------+
+   | GNB1   | KLHL17 | MECP2 | MUTYH   | NPHP4 |
+   +--------+--------+-------+---------+-------+
+   | OR4F5  | PBX1   | PRCC  | PTEN    | RER1  |
+   +--------+--------+-------+---------+-------+
+   | SAMD11 | SET    | SIRT1 | SMARCE1 | SOX2  |
+   +--------+--------+-------+---------+-------+
+   | TMEM52 | TP53   | TPM3  | USP8    | XPO1  |
+   +--------+--------+-------+---------+-------+
+
+For each individual human whole-genome, we **sampled with replacement**
+10 retrocopies from our list, so that some events were shared among
+part of our subjects.
+
+.. table:: All randomly designed retrocopies for simulation. \*HE heterozygous
+   and \*HO homozygous alternate
+   :widths: auto
+
+   +---------------+------------+-----------+--------+----------+
+   | Parental gene | Chromosome | Position  | Strand | Zygosity |
+   +===============+============+===========+========+==========+
+   | AMY2B         | chr5       | 122895832 |  \-    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | ACAP3         | chr11      | 133246346 |  \+    | H0       |
+   +---------------+------------+-----------+--------+----------+
+   | ATM           | chr19      | 16443740  |  \+    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | BCL2          | chr4       | 146453786 |  \+    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | BRAF          | chr18      | 22375812  |  \-    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | BRCA1         | chr7       | 102911369 |  \-    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | BRIP1         | chr12      | 113357216 |  \-    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | DVL1          | chr5       | 54105196  |  \-    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | FANCD2        | chr3       | 121339674 |  \+    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | FAT1          | chr16      | 65659952  |  \-    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | GNB1          | chr12      | 70734022  |  \+    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | MUTYH         | chr4       | 2716745   |  \+    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | PBX1          | chr21      | 22718521  |  \-    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | PRCC          | chr1       | 190777903 |  \-    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | PTEN          | chr2       | 140252560 |  \-    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | RER1          | chr13      | 55179109  |  \+    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | SAMD11        | chr4       | 14585135  |  \+    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | SET           | chr7       | 154178578 |  \-    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | SIRT1         | chrX       | 120716688 |  \-    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | SOX2          | chr10      | 88689163  |  \-    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | TMEM52        | chr1       | 82897536  |  \+    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | TP53          | chr5       | 42938944  |  \-    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | TPM3          | chr7       | 3488208   |  \-    | HE       |
+   +---------------+------------+-----------+--------+----------+
+   | USP8          | chr7       | 41333317  |  \+    | HO       |
+   +---------------+------------+-----------+--------+----------+
+   | XPO1          | chr10      | 33172062  |  \-    | HE       |
+   +---------------+------------+-----------+--------+----------+
+
+.. table:: Parental gene name for the retrocopies sampled by individual whole-genome
+   :widths: auto
+
+   +-------+---------+------+--------+---------+
+   | IND1  | IND2    | IND3 | IND4   | IND5    |
+   +=======+=========+======+========+=========+
+   | ATM   | AMY2B   | ATM  | AMY2B  | AMY2B   |
+   +-------+---------+------+--------+---------+
+   | BCL2  | BRCA1   | GNB1 | BRAF   | BRIP1   |
+   +-------+---------+------+--------+---------+
+   | BRIP  | FANCD2  | MECP | BRIP1  | FANCD2  |
+   +-------+---------+------+--------+---------+
+   | DVL1  | FAT1    | PBX1 | DVL1   | NPHP4   |
+   +-------+---------+------+--------+---------+
+   | MECP  | KLHL17  | PRCC | FANCD2 | PTEN    |
+   +-------+---------+------+--------+---------+
+   | OR4F  | MUTYH   | PTEN | GNB1   | RER1    |
+   +-------+---------+------+--------+---------+
+   | PTEN  | RER1    | RER1 | KLHL17 | SMARCE1 |
+   +-------+---------+------+--------+---------+
+   | SET   | SET     | SAMD | MECP2  | TP53    |
+   +-------+---------+------+--------+---------+
+   | SOX2  | SMARCE1 | SIRT | SET    | TPM3    |
+   +-------+---------+------+--------+---------+
+   | XPO1  | SOX2    | XPO1 | TMEM52 | XPO1    |
+   +-------+---------+------+--------+---------+
+
+Simulation
+==========
+
+We used the tool SANDY, *A straightforward and complete next-generation sequencing read
+simulator* [1]_, for simulate all 5 genomes according to the structural variations that
+we desgined and the sampling. SANDY demands 2 steps for the task: First we indexed all
+retrocopies for each individual and next we could simulate all whole-genome sequencing.
+
+.. code-block:: sh
+
+   # Reference genome
+   REF_FASTA=hg38.fa
+
+   # Coverage depth
+   DEPTH=40
+
+   # Retrocopies by individual
+   IND=(ind1.txt ind2.txt ind3.txt ind4.txt ind5.txt)
+
+   # Index all retrocopies
+   for ind in "${IND[@]}"; do
+     sandy variation add --structural-variation=${ind%%.txt} $ind
+   done
+
+   # Simulate all genomes
+   for ind in "${IND[@]}"; do
+     sandy_index=${ind%%.txt}
+     sandy genome \
+       --id='%i.%U_%c:%S-%E_%v' \
+       --structural-variation=$sandy_index \
+       --output-dir=$sandy_index \
+       --jobs=20 \
+       --seed=42 \
+       --quality-profile='hiseq_101' \
+       --coverage=$DEPTH \
+       --verbose \
+       $REF_FASTA
+   done
+
+
+References and Further Reading
+==============================
+
+.. [1] Miller, Thiago et al. (2019).
+   galantelab/sandy: Release v0.23 (Version v0.23).
+   Zenodo. http://doi.org/10.5281/zenodo.2589575.