estimateScore: estimateScore

In IOBR/IOBR: Immune Oncology Biological Research

estimateScore

Description

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

# Path to input and output files
input_file <- "path/to/input.gct"
output_file <- "path/to/output.gct"

# Perform score estimation for Affymetrix platform
estimateScore(input.ds = input_file, output.ds = output_file, platform = "affymetrix")

IOBR/IOBR documentation built on Sept. 9, 2024, 8:36 p.m.