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
eset_stad <- load_data("eset_stad")
anno_grch38 <- load_data("anno_grch38")
eset <- anno_eset(eset = eset_stad, annotation = anno_grch38, probe = "id")
#> ℹ Row number of original eset: 60483
#> ✔ 100% of probes in expression set were annotated
#> ℹ Found 2293 duplicate symbols, using "mean" method
#> ℹ Row number after filtering duplicated gene symbol: 50181
eset <- as.data.frame(eset)
eset <- tibble::rownames_to_column(eset, var = "symbol")
input_file <- tempfile(pattern = "estimate_", fileext = ".gct")
output_file <- tempfile(pattern = "estimate_score_", fileext = ".gct")
writeLines(c("#1.2", paste(nrow(eset), ncol(eset) - 1, sep = "\t")), input_file)
utils::write.table(
eset,
input_file,
sep = "\t", row.names = FALSE, col.names = TRUE, append = TRUE, quote = FALSE
)
#> Warning: appending column names to file
estimateScore(input.ds = input_file, output.ds = output_file, platform = "affymetrix")
#> [1] "1 gene set: StromalSignature overlap= 138"
#> [1] "2 gene set: ImmuneSignature overlap= 140"