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MGI markers

Source: R/markers.R
markers.Rd

markers() provides a data set of MGI markers that have a current associated genomic location. By current we mean as of 27 May 2024.

Use the query parameter to retrieve only a subset of the data. The query can be any of:

  • marker identifier, if var is "mrk_id" (default);

  • marker symbol, if var is "mrk_symbol";

  • Entrez gene identifier, if var is "entrez_gene_id";

  • Ensembl gene identifier, if var is "ensembl_gene_id".

Usage

markers(
  query,
  var = c("mrk_id", "mrk_symbol", "entrez_gene_id", "ensembl_gene_id")
)

Arguments

query

A character vector of query terms to be used in the filtering of the returned data set of MGI markers.

var

A string, one of: "mrk_id", for marker identifiers; "mrk_symbol", for marker symbols; "entrez_gene_id", for Entrez gene identifiers, or "ensembl_gene_id" for Ensembl gene identifiers.

Value

A tibble of 15 variables:

  • mrk_id: MGI marker identifier;

  • mrk_type: MGI marker type;

  • mrk_symbol: MGI marker symbol;

  • mrk_name: MGI marker name.

  • genome_build: Mouse genome build: always "GRCm39".

  • entrez_gene_id: Entrez gene identifier.

  • ncbi_gene_chr: Chromosome name, following NCBI's gene model.

  • ncbi_gene_start: Chromosome start position, following NCBI's gene model.

  • ncbi_gene_end: Chromosome end position, following NCBI's gene model.

  • ncbi_gene_strand: Chromosome strand, following NCBI's gene model.

  • ensembl_gene_id: Ensembl gene identifier.

  • ensembl_gene_chr: Chromosome name, following Ensembl's gene model.

  • ensembl_gene_start: Chromosome start position, following Ensembl's gene model.

  • ensembl_gene_end: Chromosome end position, following Ensembl's gene model.

  • ensembl_gene_strand: Chromosome strand, following Ensembl's gene model.

Examples

# All markers.
markers()
#> # A tibble: 71,489 × 15
#>    mrk_id mrk_type mrk_symbol mrk_name genome_build entrez_gene_id ncbi_gene_chr
#>    <chr>  <chr>    <chr>      <chr>    <chr>        <chr>          <chr>        
#>  1 MGI:8… Gene     a          nonagou… GRCm39       50518          2            
#>  2 MGI:8… Gene     Pzp        PZP, al… GRCm39       11287          6            
#>  3 MGI:8… Gene     Abl1       c-abl o… GRCm39       11350          2            
#>  4 MGI:8… Gene     Abl2       ABL pro… GRCm39       11352          1            
#>  5 MGI:8… Gene     Scgb1b27   secreto… GRCm39       11354          7            
#>  6 MGI:8… Gene     Scgb2b27   secreto… GRCm39       233099         7            
#>  7 MGI:8… Gene     Scgb2b26   secreto… GRCm39       110187         7            
#>  8 MGI:8… Gene     Acadl      acyl-Co… GRCm39       11363          1            
#>  9 MGI:8… Gene     Acadm      acyl-Co… GRCm39       11364          3            
#> 10 MGI:8… Gene     Acads      acyl-Co… GRCm39       11409          5            
#> # ℹ 71,479 more rows
#> # ℹ 8 more variables: ncbi_gene_start <int>, ncbi_gene_end <int>,
#> #   ncbi_gene_strand <chr>, ensembl_gene_id <chr>, ensembl_gene_chr <chr>,
#> #   ensembl_gene_start <int>, ensembl_gene_end <int>, ensembl_gene_strand <chr>

# actin, beta
markers("Actb", "mrk_symbol")
#> # A tibble: 1 × 15
#>   mrk_symbol mrk_id  mrk_type mrk_name genome_build entrez_gene_id ncbi_gene_chr
#>   <chr>      <chr>   <chr>    <chr>    <chr>        <chr>          <chr>        
#> 1 Actb       MGI:87… Gene     actin, … GRCm39       11461          5            
#> # ℹ 8 more variables: ncbi_gene_start <int>, ncbi_gene_end <int>,
#> #   ncbi_gene_strand <chr>, ensembl_gene_id <chr>, ensembl_gene_chr <chr>,
#> #   ensembl_gene_start <int>, ensembl_gene_end <int>, ensembl_gene_strand <chr>