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)
#> Warning: replacing previous import 'utils::findMatches' by
#> 'S4Vectors::findMatches' when loading 'AnnotationDbi'
#> 
#>   ---------
#>   
#>   For example usage please run: vignette('MouseFM')
#>   
#>   Github Repo: https://github.com/matmu/MouseFM
#>   MouseFM Backend: https://github.com/matmu/MouseFM-Backend  
#> 
#>   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
#>                         
#>   ---------

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 4.3.0 RC (2023-04-13 r84269)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.2 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: America/New_York
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] MouseFM_1.10.0   BiocStyle_2.28.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] KEGGREST_1.40.0         gtable_0.3.3            ggplot2_3.4.2          
#>  [4] xfun_0.39               bslib_0.4.2             rlist_0.4.6.2          
#>  [7] Biobase_2.60.0          vctrs_0.6.2             tools_4.3.0            
#> [10] bitops_1.0-7            generics_0.1.3          curl_5.0.0             
#> [13] stats4_4.3.0            tibble_3.2.1            fansi_1.0.4            
#> [16] AnnotationDbi_1.62.0    RSQLite_2.3.1           blob_1.2.4             
#> [19] pkgconfig_2.0.3         data.table_1.14.8       dbplyr_2.3.2           
#> [22] S4Vectors_0.38.0        lifecycle_1.0.3         GenomeInfoDbData_1.2.10
#> [25] compiler_4.3.0          stringr_1.5.0           Biostrings_2.68.0      
#> [28] progress_1.2.2          munsell_0.5.0           GenomeInfoDb_1.36.0    
#> [31] htmltools_0.5.5         sass_0.4.5              RCurl_1.98-1.12        
#> [34] yaml_2.3.7              tidyr_1.3.0             pillar_1.9.0           
#> [37] crayon_1.5.2            jquerylib_0.1.4         cachem_1.0.7           
#> [40] gtools_3.9.4            tidyselect_1.2.0        digest_0.6.31          
#> [43] stringi_1.7.12          purrr_1.0.1             reshape2_1.4.4         
#> [46] dplyr_1.1.2             bookdown_0.33           grid_4.3.0             
#> [49] biomaRt_2.56.0          fastmap_1.1.1           colorspace_2.1-0       
#> [52] cli_3.6.1               magrittr_2.0.3          XML_3.99-0.14          
#> [55] utf8_1.2.3              scales_1.2.1            rappdirs_0.3.3         
#> [58] filelock_1.0.2          prettyunits_1.1.1       bit64_4.0.5            
#> [61] rmarkdown_2.21          XVector_0.40.0          httr_1.4.5             
#> [64] bit_4.0.5               png_0.1-8               hms_1.1.3              
#> [67] memoise_2.0.1           evaluate_0.20           knitr_1.42             
#> [70] GenomicRanges_1.52.0    IRanges_2.34.0          BiocFileCache_2.8.0    
#> [73] rlang_1.1.0             Rcpp_1.0.10             glue_1.6.2             
#> [76] DBI_1.1.3               xml2_1.3.3              BiocManager_1.30.20    
#> [79] BiocGenerics_0.46.0     jsonlite_1.8.4          plyr_1.8.8             
#> [82] R6_2.5.1                zlibbioc_1.46.0