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.
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MouseFM")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
#>
#> ---------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 0View meta information
comment(df)
#> [1] "#Alleles of strain C57BL_6J represent the reference (ref) alleles"
#> [2] "#reference_version=GRCm38"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_1.4.2 BiocStyle_2.22.0
#>
#> loaded via a namespace (and not attached):
#> [1] Biobase_2.54.0 httr_1.4.2 tidyr_1.2.0
#> [4] sass_0.4.0 bit64_4.0.5 jsonlite_1.8.0
#> [7] gtools_3.9.2 bslib_0.3.1 assertthat_0.2.1
#> [10] BiocManager_1.30.16 stats4_4.1.2 BiocFileCache_2.2.1
#> [13] blob_1.2.2 GenomeInfoDbData_1.2.7 yaml_2.3.5
#> [16] progress_1.2.2 pillar_1.7.0 RSQLite_2.2.10
#> [19] rlist_0.4.6.2 glue_1.6.2 digest_0.6.29
#> [22] GenomicRanges_1.46.1 XVector_0.34.0 colorspace_2.0-3
#> [25] plyr_1.8.6 htmltools_0.5.2 XML_3.99-0.9
#> [28] pkgconfig_2.0.3 biomaRt_2.50.3 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_0.1.2
#> [37] IRanges_2.28.0 ggplot2_3.3.5 ellipsis_0.3.2
#> [40] cachem_1.0.6 BiocGenerics_0.40.0 cli_3.2.0
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#> [52] hms_1.1.1 lifecycle_1.0.1 stringr_1.4.0
#> [55] S4Vectors_0.32.3 munsell_0.5.0 AnnotationDbi_1.56.2
#> [58] Biostrings_2.62.0 compiler_4.1.2 jquerylib_0.1.4
#> [61] GenomeInfoDb_1.30.1 rlang_1.0.1 grid_4.1.2
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#> [67] rmarkdown_2.11 gtable_0.3.0 DBI_1.1.2
#> [70] curl_4.3.2 reshape2_1.4.4 R6_2.5.1
#> [73] knitr_1.37 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 vctrs_0.3.8
#> [82] png_0.1-7 dbplyr_2.1.1 tidyselect_1.1.2
#> [85] xfun_0.29