read_report()
imports data from an MGI report into R as a tidy data set.
You may call this function in two alternative ways:
Using
report_key
: this is the easiest approach. A report key maps to a report currently hosted at MGI, e.g.read_report("marker_list2")
readsMRK_List2.rpt
directly from MGI server into R. See Supported Reports below for options.Using
report_file
andreport_type
: this approach is more flexible as you can read directly from a file or URL.
Supported Reports
The set of currently supported reports:
reports
#> # A tibble: 13 x 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~
Arguments
- report_key
A character vector. A key used to uniquely refer to an MGI report.
- report_file
A character vector. The file path or URL to an MGI report file.
- report_type
A character vector. The type of an MGI report.
- n_max
Maximum number of lines to read.
Value
A tibble with report data in tidy format. The set of variables is dependent on the specific report requested:
For
"marker_list1"
, seevignette("marker_list1")
.For
"marker_list2"
, seevignette("marker_list2")
.For
"marker_coordinates"
, seevignette("marker_coordinates")
.For
"gene_model_coordinates"
, seevignette("gene_model_coordinates")
.For
"sequence_coordinates"
, seevignette("sequence_coordinates")
.For
"genbank_refseq_ensembl_ids"
, seevignette("genbank_refseq_ensembl_ids")
.For
"swiss_trembl_ids"
, seevignette("swiss_trembl_ids")
.For
"swiss_prot_ids"
, seevignette("swiss_prot_ids")
.For
"gene_trap_ids"
, seevignette("gene_trap_ids")
.For
"ensembl_ids"
, seevignette("ensembl_ids")
.For
"biotype_conflicts"
, seevignette("biotype_conflicts")
.For
"primers"
, seevignette("primers")
.For
"interpro_domains"
, seevignette("interpro_domains")
.