Overview
The goal of mgi.report.reader is to facilitate the import of Mouse Genome Informatics (MGI) report files into R.
Installation
install.packages("mgi.report.reader")
# Or the development version from GitHub:
# install.packages("pak")
pak::pak("patterninstitute/mgi.report.reader")Supported MGI reports
The list of currently supported MGI reports by mgi.report.reader is provided by the dataset ?reports:
library(mgi.report.reader)
reports
#> # A tibble: 13 × 4
#> report_key report_file report_type report_name
#> <chr> <chr> <chr> <chr>
#> 1 marker_list1 MRK_List1.rpt MRK_List1 Mouse Gene…
#> 2 marker_list2 MRK_List2.rpt MRK_List2 Mouse Gene…
#> 3 marker_coordinates MGI_MRK_Coord.rpt MGI_MRK_Coord MGI Marker…
#> 4 gene_model_coordinates MGI_Gene_Model_Coord.rpt MGI_Gene_Mod… MGI Gene M…
#> 5 sequence_coordinates MGI_GTGUP.gff MGI_GTGUP MGI Sequen…
#> 6 genbank_refseq_ensembl_ids MRK_Sequence.rpt MRK_Sequence MGI Marker…
#> 7 swiss_trembl_ids MRK_SwissProt_TrEMBL.rpt MRK_SwissPro… MGI Marker…
#> 8 swiss_prot_ids MRK_SwissProt.rpt MRK_SwissProt MGI Marker…
#> 9 gene_trap_ids MRK_GeneTrap.rpt MRK_GeneTrap MGI Marker…
#> 10 ensembl_ids MRK_ENSEMBL.rpt MRK_ENSEMBL MGI Marker…
#> 11 biotype_conflicts MGI_BioTypeConflict.rpt MGI_BioTypeC… MGI Marker…
#> 12 primers PRB_PrimerSeq.rpt PRB_PrimerSeq MGI Marker…
#> 13 interpro_domains MGI_InterProDomains.rpt MGI_InterPro… InterPro d…Example
Use read_report() to read any supported MGI report into R, e.g. to read MRK_List1.rpt:
(markers <- read_report("marker_list1", n_max = 10L))
#> # A tibble: 10 × 15
#> marker_status marker_type marker_id marker_symbol marker_name feature_type
#> <fct> <fct> <chr> <chr> <chr> <fct>
#> 1 O BAC/YAC end MGI:1341858 03B03F DNA segmen… BAC/YAC end
#> 2 O BAC/YAC end MGI:1341869 03B03R DNA segmen… BAC/YAC end
#> 3 O DNA Segment MGI:1337005 03.MMHAP34FRA… DNA segmen… DNA segment
#> 4 W Gene <NA> 0610005A07Rik <NA> <NA>
#> 5 O Gene MGI:1918911 0610005C13Rik RIKEN cDNA… lncRNA gene
#> 6 W Gene <NA> 0610005K03Rik <NA> <NA>
#> 7 W Gene <NA> 0610005M07Rik <NA> <NA>
#> 8 W Gene <NA> 0610006A03Rik <NA> <NA>
#> 9 W Gene <NA> 0610006A11Rik <NA> <NA>
#> 10 W Gene <NA> 0610006C01Rik <NA> <NA>
#> # ℹ 9 more variables: chromosome <fct>, start <int>, end <int>, strand <fct>,
#> # genetic_map_pos <dbl>, synonyms <list>, marker_id_now <chr>,
#> # marker_symbol_now <chr>, note <chr>
# Report file source
report_source(markers)
#> [1] "https://www.informatics.jax.org/downloads/reports/MRK_List1.rpt"
# Report file last modification date
report_last_modified(markers)
#> [1] "2024-07-01 11:51:02 GMT"Code of Conduct
Please note that the mgi.report.reader project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Disclaimer
The mgi.report.reader package is provided “as is” without any guarantees or warranty. Although the authors have made every effort to ensure the accuracy and reliability of the software and its documentation, they are not responsible for any errors, omissions, or misinterpretations. Users are advised to test the package thoroughly before relying on it in critical applications. The authors disclaim all liability for any damage or loss resulting from the use of this package. Use of the mgi.report.reader package is at the user’s own risk.
Support for reports is an ongoing process, but we welcome pull requests for quicker coverage.
Citing this package
Firstly, if you use this package please do not forget to start by citing the Mouse Genome Informatics (MGI) and Jackson Laboratory (JAX) as they are the original providers of the data here made accessible with these readers. For details on how to cite MGI resources, please refer to: https://www.informatics.jax.org/mgihome/other/citation.shtml.
To cite us, see https://www.pattern.institute/mgi.report.reader/authors.html#citation.