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title: "miRNAmeConverter-vignette"
author: "Stefan J. Haunsberger"
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The [miRBase](http://www.mirbase.org) database [@Griffiths-Jones01012004; 
@Griffiths-Jones01012006; @Griffiths-Jones01012008; @Kozomara01012011; 
@Kozomara01012014] is the official repository for miRNAs and includes a miRNA 
naming convention [@AMBROS01032003; @meyers2008criteria].
Over the years of development miRNAs have been added to, or deleted from the 
database, while some miRNA names have been changed. As a result, each version 
of the miRBase database can differ substantially from previous versions. If 
working with just one or two miRNAs, these can be manually searched on the 
miRBase website. With larger sets of miRNAs, however, this work becomes labour 
intensive and prone to mistakes.
When working with a set of miRNAs, therefore, useful information includes

* if a certain miRNA name exists in the miRBase database.
* the miRNA sequence in a certain miRBase version.
* if a given miRNA is still considered to be a miRNA.
* the miRNA names from the most recent miRBase version
* the respective miRNA name from a different miRBase version, for using other 
services, such as miRNA target databases.  

The _miRNAmeConverter_ R package has been developed for handling naming 
challenges of mature miRNAs.

In addition we have developed a web interface that enables one to use the 
`translateMiRNAName` function via web interface and is based on shiny 
([miRNAmeConverter-web](http://www.systemsmedicineireland.ie/tools/mirna-name-converter/)).

  
## 1. Introduction

The _miRNAmeConverter_ package delivers results in a fast and transparent way. 
The main functions

- check for validity of mature miRNA names,
- determine the most likely miRBase version of a given set of miRNAs and
- translate mature miRNA names to different versions (incl. sequences). 

The core function, translating miRNA names to different versions, is especially 
useful when dealing with miRNA tools other than miRBase. To retrieve targets 
from [miRTarBase](http://mirtarbase.mbc.nctu.edu.tw/index.php), for example, 
the miRNA name from version 20 is required, whereas the website 
[miRecords](http://c1.accurascience.com/miRecords/) only accepts version 17.
The miRNAmeConverter can manage large sets of miRNA names and hence can be 
easily implemented into workflows.

The data set included in the package (_miRNAs_) is a collection of human miRNA 
names. It consists of valid miRNA names (some duplicates), incorrect names and 
features used as controls in experiments, such as the RNU44 as a house keeping 
gene for HT-qPCR assay plates from Applied Biosystems.  
  
To load the package and gain access to the functions and sample dataset of the 
miRNAmeConverter package just run the following command:

```{r highlight = TRUE}
library(miRNAmeConverter)
```

#### Citing miRNAmeConverter
To give the authors professional credit for their work, please try to cite the
publication when you use the miRNAmeConverter:

```{r highlight = TRUE}
citation("miRNAmeConverter")
```

#### Vignette Info

This vignette has been generated using an R Markdown file with 
`knitr:rmarkdown` as vignette engine [@bibtex; @knitr1; @knitr2; @knitr3; 
@knitcitations].

#### Database information

The data used in the _miRNAmeConverter_ package is obtained from the 
`miRBaseVersions.db` annotation package [@mirbaseversionscite].

#### <a name="data-input"></a>miRNA name input values

According to the nomenclature used in the miRBase repository `hsa-mir-29a` is a 
stem-loop sequence name. If we substitute the 'r' by a capital 'R' it
codes for the mature 3' miRNA `hsa-miR-29a` (or `hsa-miR-29a-5p` in the current 
version). The `miRNAs` input value for the functions has to 
be in form of a `character` vector. Algorithms of the package are __not__ case 
sensitive. This has the effect, that for example in the case `hsa-mir-29a` and 
`hsa-miR-29a` as input values both will be considered as valid mature miRNA 
names.

## 2. The MiRNANameConverter class

The MiRNANameConverter class is coded in S4 style. All functions offered by 
the miRNAmeConverter package are methods of that class. The following figure
is a simplified class diagram with the exported methods and class attributes:

<!-- 
<div style="text-align:center" markdown="1">
   <img src="class-diagram.png" alt="class-diagram"
         title="Class diagram of the MiRNANameConverter class" style="width: 200px;"/>
</div>
-->
![class-diagram](class-diagram.png)

All methods can be displayed by
```{r highlight = TRUE}
ls("package:miRNAmeConverter");
```

The slot names (attributes) of the class can be displayed by
```{r highlight = TRUE}
slotNames("MiRNANameConverter");
```

An instance of the `MiRNANameConverter` class can be created by calling the 
`MiRNANameConverter` function:
```{r highlight = TRUE}
MiRNANameConverter();
```


## 3. Use Cases

### 3.1 Check for valid miRNA name

#### Valid input values

We have given a set of mature miRNA names `miRNAs` and would like to check if
the names are actual miRNA names that
are or were listed in any miRBase version. Our `miRNAs` have the following 
values:
```{r highlight=TRUE}
miRNAs = c("hsa-miR-422b", "mmu-mir-872", "gra-miR157b", "cel-miR-56*");
```
Our first step is to create an instance of the `MiRNANameConverter` class by 
calling the constructor and saving it to the
variable `nc`.
```{r highlight = TRUE}
nc = MiRNANameConverter();
```
Now we check if the names are valid names listed in any of the provided miRBase 
versions:
```{r highlight = TRUE}
checkMiRNAName(nc, miRNAs);
```

#### Mixed input values

The following set of miRNA names contains valid as well as invalid names.

```{r highlight = TRUE}
# "RNU-6" and "bpcv1-miR-B23" are not valid
miRNAs = c("hsa-miR-422b", "RNU-6", "mmu-miR-872", "gra-miR157b", "bpcv1-miR-B23", "bpcv1-miR-B1");
nc = MiRNANameConverter();    # Create MiRNANameConverter object
checkMiRNAName(nc, miRNAs);   # check names
```
This time the function prints information for the features that did not pass 
the check and therefore are not included in the return value.

### 3.2 Assess most likely miRBase version

Sometimes it is useful to know the miRBase version that a given set of miRNA 
names is from. In this case one can use the `assessVersion` function to receive 
the most likely miRBase version. The following example makes use of the 
provided `example-miRNAs`-dataset.

```{r highlight = TRUE}
nc = MiRNANameConverter();             # Create MiRNANameConverter object
assessVersion(nc, example.miRNAs);     # Assess most likely miRBase version
```
The console output shows that from the `r length(example.miRNAs)` input names 
there were `r length(unique(example.miRNAs))` unique values. Five of these 
values are not listed in any miRBase version and were neglected. The return 
value is a data.frame object with the two columns `version` and `frequency`. 
It is ordered by frequency and version. It shows that 347 out of 350 valid 
input miRNAs could be assigned to miRBase version 9.0. This is the highest 
score and therefore the most likely miRBase version of the input mature 
miRNA names.

### 3.3 Translate miRNA name(s) and their sequence(s)

Translating miRNA names to different versions is the most required function. 
Let us assume we found a paper that shows that the miRNA `"hsa-miR-422b"` is 
significantly differentially expressed under certain conditions. Assume further, 
that we did a similar experiment but this miRNA does not show up in our analysis. 
Instead we got `"hsa-miR-378a-3p"` from miRBase version 21. We see, that the 
previous paper was released a couple of years ago so there might be a chance 
that their miRNA could now run under a different name. We apply the 
`translateMiRNAName` function with `hsa-miR-422b` as miRNA parameter and no 
version. With no given version the function returns the miRBase version 21 
by default.
```{r highlight = TRUE}
miRNA.paper = "hsa-miR-422b";
nc = MiRNANameConverter();             # Create MiRNANameConverter object
translateMiRNAName(nc, miRNA.paper);   # Translate miRNA names
```

The result shows that these two miRNAs are actually the same. This is because 
`"hsa-miR-422b"` is last listed in miRBase version 9.2. In version 10.0 it was 
named `"hsa-miR-378"` which in the current version 21.0 runs under the name 
`"hsa-miR-378a-3p"`.

Another example with more diverse input names is shown below, with the 
respective console output and the entry in the attribute `description`.
```{r highlight = TRUE}
miRNAs = c("hsa-miR-128b", "hsa-miR-213", "mmu-miR-302b*", 
           "mmu-miR-872", "ebv-miR-BART5", "bpcv1-miR-B23");
nc = MiRNANameConverter();              # Create MiRNANameConverter object
result = translateMiRNAName(            # Translate names
                            nc
                            ,miRNAs
                            ,sequenceFormat = 1
                            ,versions = c(8, 8.1, 18, 21)
                            );        
```

The console output shows us that one of the input values is not a miRNA 
(`"bpcv1-miR-B23"`) and another is not listed in miRBase version 21 
(`"hsa-miR-128b"`).

```{r highlight = TRUE}
result;
```

#### Attribute `description`

The information, whether a miRNA is OK or not, is stored in form of 
an attribute of the return value of the function. This `data.frame` object 
provides information about every single input value and can be accessed via 
the `attr` command followed by `'description'`.
```{r highlight = TRUE}
attr(result, 'description');
```

#### Attribute `sequences`

Sometimes it can be useful to confirm the sequence of miRNAs for selected
miRBase versions. In such a case all we have to do is checking out the
`sequence` attribute of our translation result.
```{r highlight = TRUE}
attr(result, 'sequence');
```
Due to the fact that we called the `translateMiRNAName` function with the
parameter `sequenceFormat = 1` the attribute only contains the sequence for
each version respectively. If we would like to have miRNA name and sequence
combined in one table we can call the `translateMiRNAName` function with
`sequenceFormat = 2`.
```{r highlight = TRUE}
result = translateMiRNAName(            # Translate names
                            nc
                            ,miRNAs
                            ,sequenceFormat = 2
                            ,versions = c(17, 19, 21)
                            );
attr(result, 'sequence');
```

### 3.4 Other functions

#### Save translation results

Sometimes it is useful to save a variable to a file. Taking the translation 
`result` from above we can do so by running the following command with default 
settings:
```{r highlight = TRUE, eval=FALSE}
saveResults(nc, result);
```
Three files will be saved, the miRNA name translation result, the description 
and sequence. By default the files are tab-separated files without the parameter 
`quote` set to `FALSE`. Other options can be applied and will be passed on to 
the `utils::write.table` function.

#### Getter functions

Other functions are so called getter-functions to receive the values of the 
class attributes `current.version` and `valid.versions` respectively.
```{r highlight = TRUE}
nc = MiRNANameConverter();   # Create MiRNANameConverter object
currentVersion(nc);          # Receive the maximum miRBase version included in the package
validVersions(nc);           # Receive all valid versions
nOrganisms(nc);              # Number of organisms
validOrganisms(nc);          # Valid organisms
```

## Additional information

### Packages loaded via namespace
The following packages are used in the `miRNAmeConverter` package: 

* AnnotationDbi_1.32.3 [@annotdbicite]
* miRBaseVersions.db annotation package [@mirbaseversionscite]
* RSQLite_1.0.0 [@rsqlitecite]
* tools_3.2.5 [@toolscite]

### Future Aspects
This tool can only offer good functionality if it will be kept up to date.
Therefore we plan to include new miRBase releases as soon as possible.

## References {-}



