readResults: Reading results of enrichment analysis

In waldronlab/GSEABenchmarkeR: Reproducible GSEA Benchmarking

Reading results of enrichment analysis

Description

These functions read results obtained from the application of enrichment methods to multiple datasets for subsequent assessment.

Usage

readResults(
  data.dir,
  data.ids,
  methods,
  type = c("runtime", "ranking", "typeI")
)

Arguments

data.dir	Character. The data directory where results have been saved to.
data.ids	A character vector of dataset IDs.
methods	Methods for enrichment analysis. A character vector with method names typically chosen from sbeaMethods and nbeaMethods, or user-defined functions implementing methods for enrichment analysis.
type	Character. Type of the result. Should be one out of 'runtime', 'ranking', or 'typeI'.

Value

A result list with an entry for each method applied. Each entry stores corresponding runtimes (type="runtime" ), gene set rankings (type="ranking"), or type I error rates (type="typeI") as obtained from applying the respective method to the given datasets.

Author(s)

Ludwig Geistlinger <[e-mail]>

See Also

runEA to apply enrichment methods to multiple datasets.

Examples

    # simulated setup: 
    # 1 methods & 1 datasets
    methods <- paste0("m", 1:2)
    data.ids <- paste0("d", 1:2)

    # result directory
    res.dir <- tempdir()
    sdirs <- file.path(res.dir, methods)
    for(d in sdirs) dir.create(d)
    
    # store runtime & rankings 
    for(m in 1:2)
    {
        rt <- runif(5, min=m, max=m+1)
        for(d in 1:2)
        {
            # runtime
            out.file <- paste(data.ids[d], "txt", sep=".")
            out.file <- file.path(sdirs[m], out.file)
            cat(rt[d], file=out.file) 

            # ranking
            out.file <- sub("txt$", "rds", out.file)
            r <- EnrichmentBrowser::makeExampleData("ea.res") 
            r <- EnrichmentBrowser::gsRanking(r, signif.only=FALSE)
            saveRDS(r, file=out.file)   
        }
    }

    # reading runtime & rankings
    rts <- readResults(res.dir, data.ids, methods, type="runtime")
    rkgs <- readResults(res.dir, data.ids, methods, type="ranking")

waldronlab/GSEABenchmarkeR documentation built on Nov. 3, 2023, 10:59 p.m.