ORscraper (version 0.1.0)

filter_pathogenic_only: Filter for pathogenic results only

Description

This function filters a list of pathogenicity classifications, retaining only those marked as "Pathogenic".

Usage

filter_pathogenic_only(pathogenic_list, related_list)

Value

A list containing only the elements of the related list corresponding to "Pathogenic" classifications.

Arguments

pathogenic_list

List. A list of pathogenicity classifications.

related_list

List. A list of corresponding data to filter alongside pathogenicity.

Examples

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")
genes <- readxl::read_excel(genes_file)
mutations <- unique(genes$GEN)

TableValues <- extract_values_from_tables(lines, mutations)
mutateGenes <- TableValues[[1]]
pathogenity <- TableValues[[2]]
frequencies <- TableValues[[3]]
changes <- TableValues[[5]]

pathogenic_mutations <- filter_pathogenic_only(pathogenity, mutateGenes)
pathogenic_changes <- filter_pathogenic_only(pathogenity, changes)
pathogenic_frequencies <- filter_pathogenic_only(pathogenity, frequencies)