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
sbeaMethodsandnbeaMethods, 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.
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")