Turn a PanelApp panel detail into a table of genes — panelapp_parse

Pure.

Usage

panelapp_parse_panel(body)

Arguments

body: A parsed PanelApp panel detail response.

Value

A tibble of symbol, confidence (the raw level PanelApp sent), level ("green", "amber", "red", or NA for anything else), hgnc_id, and source_url. NULL when the panel has no genes.

Details

Every gene on the panel is returned, red included. See the note in the file header on why the confidence level is not converted to a weight here.

References

Martin et al. (2019). PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nature Genetics 51(11), 1560-1565. doi:10.1038/s41588-019-0528-2

Service documentation: https://panelapp.genomicsengland.co.uk/

Examples

body <- list(id = 255, genes = list(
  list(
    entity_name = "NF1",
    gene_data = list(gene_symbol = "NF1", hgnc_id = "HGNC:7765"),
    confidence_level = "3"
  )
))
panelapp_parse_panel(body)
#> # A tibble: 1 × 5
#>   symbol confidence level hgnc_id   source_url                                  
#>   <chr>  <chr>      <chr> <chr>     <chr>                                       
#> 1 NF1    3          green HGNC:7765 https://panelapp.genomicsengland.co.uk/pane…