estimateScore

This function reads a gene expression dataset in GCT format, calculates enrichment scores for specific gene sets, and writes the computed scores to an output file. It supports multiple platform types and performs platform-specific calculations if necessary.

Usage

estimateScore(
  input.ds,
  output.ds,
  platform = c("affymetrix", "agilent", "illumina")
)

Arguments

input.ds

A character string specifying the path to the input dataset file in GCT format. The file should have gene expression data with appropriate headers.

output.ds

A character string specifying the path to the output dataset file, where the calculated scores will be written.

platform

A character vector indicating the platform type. Must be one of "affymetrix", "agilent", or "illumina". Platform-specific calculations are performed based on this parameter.

Value

This function does not return a value but writes the computed scores to the specified output file in GCT format.

Examples

if (FALSE) { # \dontrun{
set.seed(123)
si_geneset_data <- load_data("SI_geneset")
if (!is.null(si_geneset_data)) {
  gene_names <- unique(c(si_geneset_data[1, -1], si_geneset_data[2, -1]))
  gene_names <- gene_names[!is.na(gene_names) & gene_names != ""]
  gene_names <- head(gene_names, 200)
  n_genes <- length(gene_names)
  eset_sim <- as.data.frame(matrix(rnorm(n_genes * 2, mean = 5, sd = 1), n_genes, 2))
  rownames(eset_sim) <- gene_names
  colnames(eset_sim) <- c("Sample1", "Sample2")
  eset_sim <- tibble::rownames_to_column(eset_sim, var = "symbol")
  input_file <- tempfile(pattern = "estimate_", fileext = ".gct")
  output_file <- tempfile(pattern = "estimate_score_", fileext = ".gct")
  writeLines(c("#1.2", paste(nrow(eset_sim), ncol(eset_sim) - 1, sep = "\t")), input_file)
  utils::write.table(eset_sim, input_file, sep = "\t", row.names = FALSE,
                    col.names = TRUE, append = TRUE, quote = FALSE)
  score_res <- estimateScore(input.ds = input_file, output.ds = output_file,
                             platform = "affymetrix")
  if (!isFALSE(score_res) && file.exists(output_file)) {
    head(read.table(output_file, skip = 2, header = TRUE, sep = "\t"))
  }
}
} # }