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README.md
# MouseFM: In-silico methods for finemapping of genetic regions in inbred mice [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social)](https://twitter.com/intent/tweet?hashtags=asd&url=https://www.biorxiv.org/content/...)  + [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)](https://img.shields.io/twitter/follow/_MatthiasMunz?label=Follow&style=social)\ University of L├╝beck, Germany ## License GNU General Public License v3.0