# MouseFM: In-silico methods for finemapping of genetic regions in inbred mice
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+ [Introduction](#Introduction)\
+ [Available inbred strains](#Available-inbred-strains)\
+ [Installation](#Installation)\
+ [Help pages](#Help-pages)\
+ [Authors](#Authors)\
+ [License](#License)
## Introduction
This **R** package provides methods for **genetic finemapping** in **inbred mice** by taking advantage of their **very high homozygosity rate** (>95%).
For one ore more chromosomal regions (**GRCm38**), method `finemap` extracts homozygous single nucleotide variants (SNVs) for which the allele differs between two sets of strains (e.g. case vs controls) and outputs respective causal SNV/gene candidates.
Method `prio` allows to select strain combinations which best refine a specified genetic region. E.g. if a crossing experiment with two inbred mouse strains 'strain1' and 'strain2' resulted in a QTL, the outputted strain combinations can be used to refine the respective region in further crossing experiments for selecting causal SNP/gene candidates.
Method `fetch` allows to fetch genotypes for a specific region of interest.
## Available inbred strains
| No | Strain | No | Strain | No | Strain |
|----|--------------------|----|-----------|----|-------------|
| 1 | 129P2/OlaHsd | 14 | C57BR/cdJ | 27 | NOD/ShiLtJ |
| 2 | 129S1/SvImJ | 15 | C57L/J | 28 | NZB/B1NJ |
| 3 | 129S5/SvEvBrd | 16 | C58/J | 29 | NZO/HlLtJ |
| 4 | A/J | 17 | CAST/EiJ | 30 | NZW/LacJ |
| 5 | AKR/J | 18 | CBA/J | 31 | PWK/PhJ |
| 6 | BALB/cJ | 19 | DBA/1J | 32 | RF/J |
| 7 | BTBR T + Itpr3tf/J | 20 | DBA/2J | 33 | SEA/GnJ |
| 8 | BUB/BnJ | 21 | FVB/NJ | 34 | SPRET/EiJ |
| 9 | C3H/HeH | 22 | I/LnJ | 35 | ST/bJ |
| 10 | C3H/HeJ | 23 | KK/HiJ | 36 | WSB/EiJ |
| 11 | C57BL/10J | 24 | LEWES/EiJ | 37 | ZALENDE/EiJ |
| 12 | C57BL/6 | 25 | LP/J | | |
| 13 | C57BL/6NJ | 26 | MOLF/EiJ | | |
Variation data was taken from the **Mouse Genomes Project** (https://www.sanger.ac.uk/data/mouse-genomes-project/).
## Installation
```R
devtools::install_github('matmu/MouseFM', build_vignettes = TRUE)
```
Loading package
```{r}
library(MouseFM)
```
**Please note**: A valid internet connection (HTTP port: 80) is required in order to install and use the package.
## Help pages
Multiple vignettes exist that guide you through general functionality of **MouseFM**.
```R
browseVignettes("MouseFM")
```
To see the help pages for each specific funtion:
```R
help(package="MouseFM")
```
## Authors
Matthias Munz [](https://img.shields.io/twitter/follow/_MatthiasMunz?label=Follow&style=social)\
University of Lübeck, Germany
## License
GNU General Public License v3.0
