ORscraper (version 0.1.0)

search_ncbi_clinvar: Search for pathogenicity information in NCBI ClinVar

Description

This function queries the NCBI ClinVar database for germline classifications based on gene and codification data.

Usage

search_ncbi_clinvar(pathogenicity, genes_mutated, total_codifications)

Value

An updated list of pathogenicity classifications based on NCBI ClinVar search results.

Arguments

pathogenicity

Ordered list. Existing pathogenicity data.

genes_mutated

Ordered list. Existing mutated gene data.

total_codifications

Ordered list. Existing mutated gen codification data.

Examples

# \donttest{
InputPath <- system.file("extdata", package = "ORscraper")
files <- read_pdf_files(InputPath)
lines <- read_pdf_content(files[1])  # Example with the first file

genes_file <- system.file("extdata/Genes.xlsx", package = "ORscraper")

if (requireNamespace("readxl", quietly = TRUE)) {
  genes <- readxl::read_excel(genes_file)
  mutations <- unique(genes$GEN)

  TableValues <- extract_values_from_tables(lines, mutations)
  mutateGenes <- TableValues[[1]]
  pathogenity <- TableValues[[2]]
  codifications <- TableValues[[4]]

  search_pathogenity <- search_ncbi_clinvar(pathogenity, mutateGenes, codifications)
}
# }