Prioritization of inbred mouse strains for resolving genetic regions

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

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

Introduction

This R package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%).

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 and to select candidate genes.

Installation

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MouseFM")

Loading package

library(MouseFM)

Example function calls

Available mouse strains

avail_strains()

Prioritize additional mouse strains for a given region which was identified in a crossing experiment with strain1 C57BL_6J and strain2 AKR_J.

df = prio("chr1", start=5000000, end=6000000, strain1="C57BL_6J", strain2="AKR_J")

View meta information

comment(df)

Extract the combinations with the best refinement

get_top(df$reduction, n_top=3)

Create plots

plots = vis_reduction_factors(df$genotypes, df$reduction, 2)
plots[[1]]
plots[[2]]

Output of Session Info

The output of sessionInfo() on the system on which this document was compiled:

sessionInfo()

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