List Marker Positions

Retrieves marker placements on genome maps from /markerpositions. A position here is relative to a named brapi_map() (genetic, in cM, or physical, in bp) - a different coordinate system from brapi_variants()'s start/referenceName, which places a variant on a reference assembly instead. A server may populate either, both, or neither; one being empty does not imply the other is.

Usage

brapi_marker_positions(
  con,
  mapDbId = NULL,
  variantDbId = NULL,
  linkageGroupName = NULL,
  minPosition = NULL,
  maxPosition = NULL,
  ...
)

Arguments

con

A brapi_connection() object.

mapDbId

Character or NULL. Filter by genome map.

variantDbId

Character or NULL. Filter by a single marker/variant ID. For multiple IDs at once, use brapi_search_marker_positions() instead.

linkageGroupName

Character or NULL. Filter by linkage group (e.g. chromosome) name.

minPosition

Integer or NULL. Minimum position, inclusive.

maxPosition

Integer or NULL. Maximum position, inclusive.

...

Additional query parameters.

Value

A tibble with one row per marker placement.

BrAPI endpoint

GET /markerpositions - see the v2.1 specification.

Query parameters the specification defines, which may be passed through ...:

mapDbId, linkageGroupName, variantDbId, minPosition, maxPosition.

Examples

# \donttest{
con <- brapi_connection("https://test-server.brapi.org")
brapi_marker_positions(con, mapDbId = "genome_map1")
#> # A tibble: 3 × 7
#>   additionalInfo   linkageGroupName mapDbId     mapName     position variantDbId
#>   <list>           <chr>            <chr>       <chr>          <int> <chr>      
#> 1 <named list [1]> Chromosome 1     genome_map1 Primary Pa…      200 variant01  
#> 2 <named list [1]> Chromosome 1     genome_map1 Primary Pa…     4000 variant02  
#> 3 <named list [1]> Chromosome 1     genome_map1 Primary Pa…    60000 variant03  
#> # ℹ 1 more variable: variantName <chr>
# }