README.md

In MouseFM: In-silico methods for genetic finemapping in inbred mice

MouseFM: In-silico methods for finemapping of genetic regions in inbred mice

 + Introduction\  + Available inbred strains\  + Installation\  + Help pages\  + Authors\  + 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

devtools::install_github('matmu/MouseFM', build_vignettes = TRUE)

Loading package

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.

browseVignettes("MouseFM")

To see the help pages for each specific funtion:

help(package="MouseFM")

Authors

Matthias Munz \ University of Lübeck, Germany

License

GNU General Public License v3.0

MouseFM documentation built on Nov. 8, 2020, 7:26 p.m.