Export data from R

Usage

export(object, con, ...)

# S4 method for class 'FgseaList,character'
export(
  object,
  con,
  geneSetResults = FALSE,
  compress = FALSE,
  overwrite = TRUE,
  quiet = FALSE
)

Arguments

object: Object.
con: character(1). Directory path.
geneSetResults: logical(1) or character. Export per-gene set expression including log fold change values generated from DESeq2. Can be slow when processing all MSigDB collections, so disabled by default. Alternatively, can declare specific collections to process (see collectionNames for supported values).
compress: logical(1). Apply gzip compression to all files.
overwrite: logical(1). Overwrite existing file on disk.
quiet: logical(1). Perform command quietly, suppressing messages.
...: Additional arguments.

Value

Invisible character or list of file paths.

Note

Updated 2023-09-13.

On-disk structure

Example:

file.path("object", "mutant_vs_control", "c1.csv")

S4 object is currently structured by:

Gene set (c1-c8, h).
Contrast.

The object was structured in this manner to flow with the R Markdown template. However, when writing to disk, I think it makes more sense to organize by:

Contrast
Gene set.

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
con <- AcidBase::tempdir2()
#> Error in vapply(X = X, FUN = FUN, FUN.VALUE = logical(1L), ..., USE.NAMES = useNames): formal argument "USE.NAMES" matched by multiple actual arguments
out <- export(
    object = object,
    con = con
)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'con' in selecting a method for function 'export': object 'con' not found
print(out)
#> Error: object 'out' not found
AcidBase::unlink2(con)
#> Error: object 'con' not found