Convenience function that retrieves marker positions on a genome map as
a tidy tibble. Positions come from the Genome Maps entity
(brapi_marker_positions() / /markerpositions), which places a
marker on a named brapi_map() - genetic (cM) or physical (bp), per
the map's type and unit - not from brapi_variants()'s
start/referenceName, which places a variant on a reference assembly
instead. A server may populate either, both, or neither; the two are
independent coordinate systems, not duplicates of each other.
Arguments
- con
A
brapi_connection()object.- variantSetDbId
Character or NULL. A variant set to retrieve marker positions for. Mutually exclusive with
mapDbId.- mapDbId
Character or NULL. A single genome map to retrieve all marker positions from. Mutually exclusive with
variantSetDbId.
Value
A tibble with columns variantDbId, variantName, mapDbId,
mapName, type, unit, linkageGroupName, and position - one
row per marker-map placement, so a marker on several maps appears
more than once. type and unit are joined in from brapi_maps()
so a caller can tell a genetic (cM) map from a physical (bp) one.
Details
Supply exactly one of mapDbId (every marker placed on that one map)
or variantSetDbId (positions for every variant in that set, wherever
they have been placed). The variantSetDbId path looks variant IDs up
first via brapi_variants(), then retrieves their positions in one
call via brapi_search_marker_positions() rather than the GET
/markerpositions filter, which only accepts a single variantDbId.
If a marker is placed on more than one map, it contributes one row per placement - the result is never collapsed to one row per marker.
Examples
# \donttest{
con <- brapi_connection("https://test-server.brapi.org")
brapi_get_marker_map(con, mapDbId = "genome_map1")
#> # A tibble: 3 × 8
#> variantDbId variantName mapDbId mapName type unit linkageGroupName position
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 variant01 M1 genome_… Primar… Phys… cM Chromosome 1 200
#> 2 variant02 M2 genome_… Primar… Phys… cM Chromosome 1 4000
#> 3 variant03 M3 genome_… Primar… Phys… cM Chromosome 1 60000
brapi_get_marker_map(con, variantSetDbId = "variantset1")
#> ℹ Async search started (ID: c1c6efdc-06fa-4d97-957b-ee20149e4bf8). Polling...
#> Warning: 14 of 20 variants in "variantset1" have no marker position record; returning
#> positions for the remaining 6.
#> # A tibble: 6 × 8
#> variantDbId variantName mapDbId mapName type unit linkageGroupName position
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 variant01 M1 genome_… Primar… Phys… cM Chromosome 1 200
#> 2 variant02 M2 genome_… Primar… Phys… cM Chromosome 1 4000
#> 3 variant03 M3 genome_… Primar… Phys… cM Chromosome 1 60000
#> 4 variant04 M4 genome_… Primar… Phys… cM Chromosome 2 200
#> 5 variant05 M5 genome_… Primar… Phys… cM Chromosome 2 4000
#> 6 variant06 M6 genome_… Primar… Phys… cM Chromosome 2 60000
# }