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Parse the ClinGen gene-validity CSV

Source: R/clingen_validity.R
clingen_parse_validity.Rd

Pure. Takes the file as a single string, the way biohttp::get_text() returns it.

Usage

clingen_parse_validity(text)

Arguments

text

The CSV file contents.

Value

A tibble of gene, hgnc, disease, mondo, moi, classification, sop, panel, date, and source_url, one row per curation. A gene appears once per disease it has been curated against. NULL when the file is empty or carries no header.

References

Strande et al. (2017). Evaluating the clinical validity of gene-disease associations: an evidence-based framework developed by the Clinical Genome Resource. The American Journal of Human Genetics 100(6), 895-906. doi:10.1016/j.ajhg.2017.04.015

Service documentation: https://search.clinicalgenome.org/

Examples

text <- paste(
  '"CLINGEN GENE DISEASE VALIDITY CURATIONS","",""',
  '"+++","+++","+++"',
  '"GENE SYMBOL","DISEASE LABEL","CLASSIFICATION"',
  '"+++","+++","+++"',
  '"NF1","neurofibromatosis type 1","Definitive"',
  sep = "\n"
)
clingen_parse_validity(text)
#> # A tibble: 1 × 10
#>   gene  hgnc  disease    mondo moi   classification sop   panel date  source_url
#>   <chr> <chr> <chr>      <chr> <chr> <chr>          <chr> <chr> <chr> <chr>     
#> 1 NF1   NA    neurofibr… NA    NA    Definitive     NA    NA    NA    NA