filterCommonGenes — filterCommonGenes • IOBR

This function filters and merges a dataset with a set of common genes.

Usage

filterCommonGenes(input.f, output.f, id = c("GeneSymbol", "EntrezID"))

Arguments

input.f: A character string specifying the path to the input file or a connection object. The file should be a tab-separated table with row names.
output.f: A character string specifying the path to the output file.
id: A character string indicating the type of gene identifier to use. Can be either "GeneSymbol" or "EntrezID".

Value

No return value. The function writes the merged dataset to the specified output file.

Examples

# Create a sample common_genes dataframe
common_genes <- data.frame(
  GeneSymbol = c("BRCA1", "TP53", "EGFR"),
  stringsAsFactors = FALSE
)

# Create a sample input dataframe
input_data <- data.frame(
  GeneSymbol = c("BRCA1", "TP53", "EGFR", "NOTCH1"),
  Value = c(10, 15, 8, 12),
  stringsAsFactors = FALSE
)

# Write the input data to temporary file
input_file <- tempfile(fileext = ".txt")
output_file <- tempfile(fileext = ".txt")
write.table(input_data,
  file = input_file, sep = "\t", row.names = TRUE,
  quote = FALSE
)

# Call the filterCommonGenes function
# Note: This example requires IOBR::common_genes data
# filterCommonGenes(input_file, output_file, id = "GeneSymbol")