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 4.2.1 (2022-06-23)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.5 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_1.8.0 BiocStyle_2.26.0
#>
#> loaded via a namespace (and not attached):
#> [1] Biobase_2.58.0 httr_1.4.4 tidyr_1.2.1
#> [4] sass_0.4.2 bit64_4.0.5 jsonlite_1.8.3
#> [7] gtools_3.9.3 bslib_0.4.0 assertthat_0.2.1
#> [10] BiocManager_1.30.19 stats4_4.2.1 BiocFileCache_2.6.0
#> [13] blob_1.2.3 GenomeInfoDbData_1.2.9 yaml_2.3.6
#> [16] progress_1.2.2 pillar_1.8.1 RSQLite_2.2.18
#> [19] rlist_0.4.6.2 glue_1.6.2 digest_0.6.30
#> [22] GenomicRanges_1.50.0 XVector_0.38.0 colorspace_2.0-3
#> [25] plyr_1.8.7 htmltools_0.5.3 XML_3.99-0.12
#> [28] pkgconfig_2.0.3 biomaRt_2.54.0 bookdown_0.29
#> [31] zlibbioc_1.44.0 purrr_0.3.5 scales_1.2.1
#> [34] tibble_3.1.8 KEGGREST_1.38.0 generics_0.1.3
#> [37] IRanges_2.32.0 ggplot2_3.3.6 ellipsis_0.3.2
#> [40] cachem_1.0.6 BiocGenerics_0.44.0 cli_3.4.1
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#> [46] evaluate_0.17 fansi_1.0.3 xml2_1.3.3
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#> [52] hms_1.1.2 lifecycle_1.0.3 stringr_1.4.1
#> [55] S4Vectors_0.36.0 munsell_0.5.0 AnnotationDbi_1.60.0
#> [58] Biostrings_2.66.0 compiler_4.2.1 jquerylib_0.1.4
#> [61] GenomeInfoDb_1.34.0 rlang_1.0.6 grid_4.2.1
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#> [67] rmarkdown_2.17 gtable_0.3.1 DBI_1.1.3
#> [70] curl_4.3.3 reshape2_1.4.4 R6_2.5.1
#> [73] knitr_1.40 dplyr_1.0.10 fastmap_1.1.0
#> [76] bit_4.0.4 utf8_1.2.2 filelock_1.0.2
#> [79] stringi_1.7.8 Rcpp_1.0.9 vctrs_0.5.0
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#> [85] xfun_0.34