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)

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 4.1.2 (2021-11-01)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.14-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_1.4.1    BiocStyle_2.22.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] Biobase_2.54.0         httr_1.4.2             tidyr_1.1.4           
#>  [4] sass_0.4.0             bit64_4.0.5            jsonlite_1.7.2        
#>  [7] gtools_3.9.2           bslib_0.3.1            assertthat_0.2.1      
#> [10] BiocManager_1.30.16    stats4_4.1.2           BiocFileCache_2.2.0   
#> [13] blob_1.2.2             GenomeInfoDbData_1.2.7 yaml_2.2.1            
#> [16] progress_1.2.2         pillar_1.6.4           RSQLite_2.2.8         
#> [19] rlist_0.4.6.2          glue_1.5.0             digest_0.6.28         
#> [22] GenomicRanges_1.46.0   XVector_0.34.0         colorspace_2.0-2      
#> [25] plyr_1.8.6             htmltools_0.5.2        XML_3.99-0.8          
#> [28] pkgconfig_2.0.3        biomaRt_2.50.0         bookdown_0.24         
#> [31] zlibbioc_1.40.0        purrr_0.3.4            scales_1.1.1          
#> [34] tibble_3.1.6           KEGGREST_1.34.0        generics_0.1.1        
#> [37] IRanges_2.28.0         ggplot2_3.3.5          ellipsis_0.3.2        
#> [40] cachem_1.0.6           BiocGenerics_0.40.0    magrittr_2.0.1        
#> [43] crayon_1.4.2           memoise_2.0.0          evaluate_0.14         
#> [46] fansi_0.5.0            xml2_1.3.2             tools_4.1.2           
#> [49] data.table_1.14.2      prettyunits_1.1.1      hms_1.1.1             
#> [52] lifecycle_1.0.1        stringr_1.4.0          S4Vectors_0.32.2      
#> [55] munsell_0.5.0          AnnotationDbi_1.56.2   Biostrings_2.62.0     
#> [58] compiler_4.1.2         jquerylib_0.1.4        GenomeInfoDb_1.30.0   
#> [61] rlang_0.4.12           grid_4.1.2             RCurl_1.98-1.5        
#> [64] rappdirs_0.3.3         bitops_1.0-7           rmarkdown_2.11        
#> [67] gtable_0.3.0           DBI_1.1.1              curl_4.3.2            
#> [70] reshape2_1.4.4         R6_2.5.1               knitr_1.36            
#> [73] dplyr_1.0.7            fastmap_1.1.0          bit_4.0.4             
#> [76] utf8_1.2.2             filelock_1.0.2         stringi_1.7.5         
#> [79] Rcpp_1.0.7             vctrs_0.3.8            png_0.1-7             
#> [82] dbplyr_2.1.1           tidyselect_1.1.1       xfun_0.28