Prioritization of inbred mouse strains for resolving genetic regions
8 September 2024
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 prio allows to select strain combinations which best refine a specified genetic region. E.g. if a crossing experiment with two inbred mouse strains ‘strain1’ and ‘strain2’ resulted in a QTL, the outputted strain combinations can be used to refine the respective region in further crossing experiments and to select candidate genes.
2 Installation
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MouseFM")3 Loading package
library(MouseFM)4 Example function calls
Available mouse strains
avail_strains()
#> id strain
#> 1 129P2_OlaHsd 129P2/OlaHsd
#> 2 129S1_SvImJ 129S1/SvImJ
#> 3 129S5SvEvBrd 129S5/SvEvBrd
#> 4 A_J A/J
#> 5 AKR_J AKR/J
#> 6 BALB_cJ BALB/cJ
#> 7 BTBR BTBR
#> 8 BUB_BnJ BUB/BnJ
#> 9 C3H_HeH C3H/HeH
#> 10 C3H_HeJ C3H/HeJ
#> 11 C57BL_10J C57BL/10J
#> 12 C57BL_6J C57BL/6J
#> 13 C57BL_6NJ C57BL/6NJ
#> 14 C57BR_cdJ C57BR/cdJ
#> 15 C57L_J C57L/J
#> 16 C58_J C58/J
#> 17 CAST_EiJ CAST/EiJ
#> 18 CBA_J CBA/J
#> 19 DBA_1J DBA/1J
#> 20 DBA_2J DBA/2J
#> 21 FVB_NJ FVB/NJ
#> 22 I_LnJ I/LnJ
#> 23 KK_HiJ KK/HiJ
#> 24 LEWES_EiJ LEWES/EiJ
#> 25 LP_J LP/J
#> 26 MOLF_EiJ MOLF/EiJ
#> 27 NOD_ShiLtJ NOD/ShiLtJ
#> 28 NZB_B1NJ NZB/B1NJ
#> 29 NZO_HlLtJ NZO/HlLtJ
#> 30 NZW_LacJ NZW/LacJ
#> 31 PWK_PhJ PWK/PhJ
#> 32 RF_J RF/J
#> 33 SEA_GnJ SEA/GnJ
#> 34 SPRET_EiJ SPRET/EiJ
#> 35 ST_bJ ST/bJ
#> 36 WSB_EiJ WSB/EiJ
#> 37 ZALENDE_EiJ ZALENDE/EiJPrioritize additional mouse strains for a given region which was identified in a crossing experiment with strain1 C57BL_6J and strain2 AKR_J.
df = prio("chr1", start=5000000, end=6000000, strain1="C57BL_6J", strain2="AKR_J")
#> Query chr1:5,000,000-6,000,000
#> Calculate reduction factors...
#> Set size 1: 35 combinations
#> Set size 1: continue with 20 of 35 strains
#> Set size 2: 190 combinations
#> Set size 3: 1,140 combinationsView meta information
comment(df)
#> NULLExtract the combinations with the best refinement
get_top(df$reduction, n_top=3)
#> strain1 strain2 combination mean min max n
#> 8 C57BL_6J AKR_J C3H_HeH,DBA_1J,SPRET_EiJ 0.8068057 0.7467057 0.9926794 3
#> 7 C57BL_6J AKR_J C3H_HeH,DBA_2J,SPRET_EiJ 0.8068057 0.7467057 0.9926794 3
#> 6 C57BL_6J AKR_J C3H_HeJ,DBA_1J,SPRET_EiJ 0.8068057 0.7467057 0.9926794 3Create plots
plots = vis_reduction_factors(df$genotypes, df$reduction, 2)
plots[[1]]
plots[[2]]
5 Output of Session Info
The output of sessionInfo() on the system
on which this document was compiled:
sessionInfo()
#> R version 4.4.1 (2024-06-14)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.19-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_1.14.6 BiocStyle_2.32.1
#>
#> loaded via a namespace (and not attached):
#> [1] tidyselect_1.2.1 dplyr_1.1.4 farver_2.1.2
#> [4] blob_1.2.4 filelock_1.0.3 Biostrings_2.72.1
#> [7] fastmap_1.2.0 BiocFileCache_2.12.0 digest_0.6.37
#> [10] lifecycle_1.0.4 KEGGREST_1.44.1 RSQLite_2.3.7
#> [13] magrittr_2.0.3 compiler_4.4.1 rlang_1.1.4
#> [16] sass_0.4.9 progress_1.2.3 tools_4.4.1
#> [19] utf8_1.2.4 yaml_2.3.10 data.table_1.16.0
#> [22] knitr_1.48 prettyunits_1.2.0 bit_4.0.5
#> [25] curl_5.2.2 plyr_1.8.9 xml2_1.3.6
#> [28] withr_3.0.1 purrr_1.0.2 BiocGenerics_0.50.0
#> [31] grid_4.4.1 stats4_4.4.1 fansi_1.0.6
#> [34] colorspace_2.1-1 ggplot2_3.5.1 scales_1.3.0
#> [37] gtools_3.9.5 tinytex_0.52 biomaRt_2.60.1
#> [40] cli_3.6.3 rmarkdown_2.28 crayon_1.5.3
#> [43] generics_0.1.3 rlist_0.4.6.2 httr_1.4.7
#> [46] reshape2_1.4.4 DBI_1.2.3 cachem_1.1.0
#> [49] stringr_1.5.1 zlibbioc_1.50.0 AnnotationDbi_1.66.0
#> [52] BiocManager_1.30.25 XVector_0.44.0 vctrs_0.6.5
#> [55] jsonlite_1.8.8 bookdown_0.40 IRanges_2.38.1
#> [58] hms_1.1.3 S4Vectors_0.42.1 bit64_4.0.5
#> [61] magick_2.8.4 jquerylib_0.1.4 tidyr_1.3.1
#> [64] glue_1.7.0 stringi_1.8.4 gtable_0.3.5
#> [67] GenomeInfoDb_1.40.1 GenomicRanges_1.56.1 UCSC.utils_1.0.0
#> [70] munsell_0.5.1 tibble_3.2.1 pillar_1.9.0
#> [73] rappdirs_0.3.3 htmltools_0.5.8.1 GenomeInfoDbData_1.2.12
#> [76] R6_2.5.1 dbplyr_2.5.0 httr2_1.0.3
#> [79] evaluate_0.24.0 Biobase_2.64.0 highr_0.11
#> [82] png_0.1-8 memoise_2.0.1 bslib_0.8.0
#> [85] Rcpp_1.0.13 xfun_0.47 pkgconfig_2.0.3