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Read an MGI report

Source: R/read_report.R
read_report.Rd

read_report() reads in an MGI report.

Usage

read_report(
  report_file,
  report_type = c("MRK_List1", "MRK_List2", "MGI_MRK_Coord", "MGI_Gene_Model_Coord",
    "MGI_GTGUP", "MRK_Sequence", "MRK_SwissProt_TrEMBL", "MRK_SwissProt", "MRK_GeneTrap",
    "MRK_ENSEMBL", "MGI_BioTypeConflict", "PRB_PrimerSeq", "MGI_InterProDomains"),
  n_max = Inf
)

Arguments

report_file

A path or URL to an MGI report file.

report_type

Report type, one of:

  • "MRK_List1": Mouse Genetic Markers (including withdrawn marker symbols).

  • "MRK_List2": Mouse Genetic Markers (excluding withdrawn marker symbols).

  • "MGI_MRK_Coord": MGI Marker Coordinates.

  • "MGI_GTGUP": MGI Sequence Coordinates.

  • "MRK_Sequence": MGI Marker associations to Sequence (GenBank, RefSeq, Ensembl) information.

  • "MRK_SwissProt_TrEMBL": MGI Marker associations to SWISS-PROT and TrEMBL protein IDs.

  • "MRK_SwissProt": MGI Marker associations to SWISS-PROT protein IDs.

  • "MRK_GeneTrap": MGI Marker associations to Gene Trap IDs.

  • "MRK_ENSEMBL": MGI Marker associations to Ensembl sequence information.

  • "MGI_BioTypeConflict": MGI Marker associations to Ensembl or NCBI gene models where a gene vs. pseudogene discrepancy exists.

  • "PRB_PrimerSeq": MGI Marker associations with primer pairs.

  • "MGI_InterProDomains": InterPro domain associations to MGI markers.

n_max

Maximum number of lines to read.

Value

A tibble with the report data in tidy format.

Examples

base_url <- "https://www.informatics.jax.org/downloads/reports"
url <- file.path(base_url, "MRK_List1.rpt")
# Import the Mouse Genetic Markers (including withdrawn marker symbols) Report
read_report(url, "MRK_List1", n_max = 10L)
#> # A tibble: 10 × 12
#>    marker_id   marker_symbol marker_name marker_type status cM_pos chr     start
#>    <chr>       <chr>         <chr>       <fct>       <fct>   <dbl> <fct>   <int>
#>  1 MGI:1341858 03B03F        DNA segmen… BAC/YAC end O        NA   5     NA     
#>  2 MGI:1341869 03B03R        DNA segmen… BAC/YAC end O        NA   5     NA     
#>  3 MGI:1337005 03.MMHAP34FR… DNA segmen… DNA Segment O        NA   11    NA     
#>  4 NA          0610005A07Rik withdrawn,… Gene        W        NA   3     NA     
#>  5 MGI:1918911 0610005C13Rik RIKEN cDNA… Gene        O        29.4 7      4.52e7
#>  6 NA          0610005K03Rik withdrawn,… Gene        W        NA   15    NA     
#>  7 NA          0610005M07Rik withdrawn,… Gene        W        NA   6     NA     
#>  8 NA          0610006A03Rik withdrawn,… Gene        W        NA   4     NA     
#>  9 NA          0610006A11Rik withdrawn,… Gene        W        NA   NA    NA     
#> 10 NA          0610006C01Rik withdrawn,… Gene        W        NA   NA    NA     
#> # ℹ 4 more variables: end <int>, strand <fct>, feature_type <fct>,
#> #   synonyms <list>