Contents

1 Introduction

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

Method fetch allows to download homozygous genotypes of 37 inbred mouse strains for a given genetic region.

2 Installation

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

3 Loading package

library(MouseFM)
#> 
#>   ---------
#>   For example usage please run: vignette('MouseFM')
#>   
#>   Support me: http://matthiasmunz.de/support_me
#> 
#>   Citation appreciated:
#>   Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I (2021) In silico candidate variant and gene identification using inbred mouse strains. PeerJ. doi:10.7717/peerj.11017
#>   
#>   Github Repo: https://github.com/matmu/MouseFM
#>   MouseFM Backend: https://github.com/matmu/MouseFM-Backend
#>   ---------

4 Example function calls

Fetch genotypes for region chr1:5000000-6000000.

df = fetch("chr1", start=5000000, end=6000000)
#> Query chr1:5,000,000-6,000,000

df[1:10,]
#>    chr     pos        rsid ref alt most_severe_consequence
#> 1    1 5000016  rs47088541   A   T          intron_variant
#> 2    1 5000029  rs48827827   G   A          intron_variant
#> 3    1 5000057  rs48099867   C   T          intron_variant
#> 4    1 5000062 rs246021564   G   C          intron_variant
#> 5    1 5000067 rs265132353   C   T          intron_variant
#> 6    1 5000068  rs51419610   A   G          intron_variant
#> 7    1 5000101 rs253320650   C   G          intron_variant
#> 8    1 5000156        <NA>   C   T          intron_variant
#> 9    1 5000157 rs216747169   G   A          intron_variant
#> 10   1 5000240        <NA>   T   G          intron_variant
#>                                                           consequences C57BL_6J
#> 1  non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#> 2  non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#> 3  non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#> 4  non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#> 5  non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#> 6  non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#> 7  non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#> 8  non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#> 9  non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#> 10 non_coding_transcript_variant,intron_variant,NMD_transcript_variant        0
#>    129P2_OlaHsd 129S1_SvImJ 129S5SvEvBrd AKR_J A_J BALB_cJ BTBR BUB_BnJ C3H_HeH
#> 1             0           0            0     0   0       0    0       0       1
#> 2             0           0            0     0   0       0    0       0       1
#> 3             0           0            0     0   0       0    0       0       1
#> 4             0           0            0     0   0       0    0       0       1
#> 5             0           0            0     0   0       0    0       0       1
#> 6             0           0            0     0   0       0    0       0       1
#> 7             0           0            0     0   0       0    0       0       1
#> 8             0           0            0     0   0       0    0       0       0
#> 9             0           0            0     0   0       0    0       0       1
#> 10            0           0            0     0   0       0    0       0       0
#>    C3H_HeJ C57BL_10J C57BL_6NJ C57BR_cdJ C57L_J C58_J CAST_EiJ CBA_J DBA_1J
#> 1        1         0         0         0      0     0        1     1      1
#> 2        1         0         0         0      0     0        0     1      1
#> 3        1         0         0         0      0     0        0     1      1
#> 4        1         0         0         0      0     0        0     1      1
#> 5        1         0         0         0      0     0        0     1      1
#> 6        1         0         0         0      0     0        0     1      1
#> 7        1         0         0         0      0     0        0     1      1
#> 8        0         0         0         0      0     0        0     0      0
#> 9        1         0         0         0      0     0        0     1      0
#> 10       0         0         0         0      0     0        0     0      0
#>    DBA_2J FVB_NJ I_LnJ KK_HiJ LEWES_EiJ LP_J MOLF_EiJ NOD_ShiLtJ NZB_B1NJ
#> 1       1      0     0      0         1    0        0          0        1
#> 2       1      0     0      0         1    0        0          0        0
#> 3       1      0     0      0         1    0        0          0        0
#> 4       1      0     0      0         1    0        0          0        0
#> 5       1      0     0      0         1    0        0          0        0
#> 6       1      0     0      0         1    0        0          0        0
#> 7       1      0     0      0         1    0        0          0        0
#> 8       0      0     0      0         0    0        0          0        1
#> 9       0      0     0      0         1    0        0          0        0
#> 10      0      0     0      0         0    0        0          0        1
#>    NZO_HlLtJ NZW_LacJ PWK_PhJ RF_J SEA_GnJ SPRET_EiJ ST_bJ WSB_EiJ ZALENDE_EiJ
#> 1          0        0       1    1       0         1     0       1           1
#> 2          0        0       1    1       0         1     0       1           1
#> 3          0        0       1    1       0         1     0       1           1
#> 4          0        0       1    1       0         1     0       1           1
#> 5          0        0       1    1       0         0     0       1           1
#> 6          0        0       1    1       0         1     0       1           1
#> 7          0        0       1    1       0         1     0       1           1
#> 8          0        0       0    0       0         0     0       0           0
#> 9          0        0       0    1       0         0     0       1           1
#> 10         0        0       0    0       0         0     0       0           0

View meta information

comment(df)
#> [1] "#Alleles of strain C57BL_6J represent the reference (ref) alleles"
#> [2] "#reference_version=GRCm38"

5 Output of Session Info

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

sessionInfo()
#> R version 4.5.0 (2025-04-11 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows Server 2022 x64 (build 20348)
#> 
#> Matrix products: default
#>   LAPACK version 3.12.1
#> 
#> locale:
#> [1] LC_COLLATE=C                          
#> [2] LC_CTYPE=English_United States.utf8   
#> [3] LC_MONETARY=English_United States.utf8
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.utf8    
#> 
#> time zone: America/New_York
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] MouseFM_1.19.0   BiocStyle_2.37.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] KEGGREST_1.49.0      gtable_0.3.6         ggplot2_3.5.2       
#>  [4] xfun_0.52            bslib_0.9.0          httr2_1.1.2         
#>  [7] rlist_0.4.6.2        Biobase_2.69.0       vctrs_0.6.5         
#> [10] tools_4.5.0          generics_0.1.4       stats4_4.5.0        
#> [13] curl_6.2.3           tibble_3.2.1         AnnotationDbi_1.71.0
#> [16] RSQLite_2.4.0        blob_1.2.4           pkgconfig_2.0.3     
#> [19] data.table_1.17.4    RColorBrewer_1.1-3   dbplyr_2.5.0        
#> [22] S4Vectors_0.47.0     lifecycle_1.0.4      farver_2.1.2        
#> [25] compiler_4.5.0       stringr_1.5.1        Biostrings_2.77.1   
#> [28] progress_1.2.3       GenomeInfoDb_1.45.4  htmltools_0.5.8.1   
#> [31] sass_0.4.10          yaml_2.3.10          tidyr_1.3.1         
#> [34] pillar_1.10.2        crayon_1.5.3         jquerylib_0.1.4     
#> [37] cachem_1.1.0         gtools_3.9.5         tidyselect_1.2.1    
#> [40] digest_0.6.37        stringi_1.8.7        purrr_1.0.4         
#> [43] reshape2_1.4.4       dplyr_1.1.4          bookdown_0.43       
#> [46] grid_4.5.0           biomaRt_2.65.0       fastmap_1.2.0       
#> [49] cli_3.6.5            magrittr_2.0.3       dichromat_2.0-0.1   
#> [52] scales_1.4.0         prettyunits_1.2.0    filelock_1.0.3      
#> [55] UCSC.utils_1.5.0     rappdirs_0.3.3       bit64_4.6.0-1       
#> [58] rmarkdown_2.29       XVector_0.49.0       httr_1.4.7          
#> [61] bit_4.6.0            png_0.1-8            hms_1.1.3           
#> [64] memoise_2.0.1        evaluate_1.0.3       knitr_1.50          
#> [67] GenomicRanges_1.61.0 IRanges_2.43.0       BiocFileCache_2.99.5
#> [70] rlang_1.1.6          Rcpp_1.0.14          glue_1.8.0          
#> [73] DBI_1.2.3            BiocManager_1.30.25  xml2_1.3.8          
#> [76] BiocGenerics_0.55.0  jsonlite_2.0.0       plyr_1.8.9          
#> [79] R6_2.6.1