Finemapping of genetic regions in inbred mice

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

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
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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 SNVs for which the allele differs between two sets of strains (e.g. case vs controls) and outputs respective causal SNV/gene candidates.

Installation

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

Loading package

library(MouseFM)

Example function calls

Available mouse strains

avail_strains()

Call finemap to finemap a specific region

res = finemap(chr="chr7",
              strain1=c("C57BL_6J","C57L_J","CBA_J","NZB_B1NJ"),
              strain2=c("C3H_HEJ","MOLF_EiJ","NZW_LacJ","WSB_EiJ","SPRET_EiJ"),
              impact=c("HIGH", "MODERATE", "LOW"))

res[1:10,]

View meta information

comment(res)

Annotate with consequences (Not recommended for large queries!)

cons = annotate_consequences(res, "mouse")

Annotate with genes

genes = annotate_mouse_genes(res, flanking = 50000)

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.