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')
#>   
#>   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 4.2.0 RC (2022-04-21 r82226)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.4 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
#> 
#> 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       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] MouseFM_1.7.0    BiocStyle_2.25.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] Biobase_2.57.0         httr_1.4.2             tidyr_1.2.0           
#>  [4] sass_0.4.1             bit64_4.0.5            jsonlite_1.8.0        
#>  [7] gtools_3.9.2           bslib_0.3.1            assertthat_0.2.1      
#> [10] BiocManager_1.30.17    stats4_4.2.0           BiocFileCache_2.5.0   
#> [13] blob_1.2.3             GenomeInfoDbData_1.2.8 yaml_2.3.5            
#> [16] progress_1.2.2         pillar_1.7.0           RSQLite_2.2.12        
#> [19] rlist_0.4.6.2          glue_1.6.2             digest_0.6.29         
#> [22] GenomicRanges_1.49.0   XVector_0.37.0         colorspace_2.0-3      
#> [25] plyr_1.8.7             htmltools_0.5.2        XML_3.99-0.9          
#> [28] pkgconfig_2.0.3        biomaRt_2.53.0         bookdown_0.26         
#> [31] zlibbioc_1.43.0        purrr_0.3.4            scales_1.2.0          
#> [34] tibble_3.1.6           KEGGREST_1.37.0        generics_0.1.2        
#> [37] IRanges_2.31.0         ggplot2_3.3.5          ellipsis_0.3.2        
#> [40] cachem_1.0.6           BiocGenerics_0.43.0    cli_3.3.0             
#> [43] magrittr_2.0.3         crayon_1.5.1           memoise_2.0.1         
#> [46] evaluate_0.15          fansi_1.0.3            xml2_1.3.3            
#> [49] tools_4.2.0            data.table_1.14.2      prettyunits_1.1.1     
#> [52] hms_1.1.1              lifecycle_1.0.1        stringr_1.4.0         
#> [55] S4Vectors_0.35.0       munsell_0.5.0          AnnotationDbi_1.59.0  
#> [58] Biostrings_2.65.0      compiler_4.2.0         jquerylib_0.1.4       
#> [61] GenomeInfoDb_1.33.0    rlang_1.0.2            grid_4.2.0            
#> [64] RCurl_1.98-1.6         rappdirs_0.3.3         bitops_1.0-7          
#> [67] rmarkdown_2.14         gtable_0.3.0           DBI_1.1.2             
#> [70] curl_4.3.2             reshape2_1.4.4         R6_2.5.1              
#> [73] knitr_1.38             dplyr_1.0.8            fastmap_1.1.0         
#> [76] bit_4.0.4              utf8_1.2.2             filelock_1.0.2        
#> [79] stringi_1.7.6          Rcpp_1.0.8.3           vctrs_0.4.1           
#> [82] png_0.1-7              dbplyr_2.1.1           tidyselect_1.1.2      
#> [85] xfun_0.30