export: Export data from R

In acidgenomics/acidgsea: Acid Genomics GSEA

Export data from R

Description

Export data from R

Usage

export(object, con, ...)

## S4 method for signature '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.

On-disk structure

Example:

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

S4 object is currently structured by:

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

2. 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:

1. Contrast

2. Gene set.

Note

Updated 2023-09-13.

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
con <- AcidBase::tempdir2()
out <- export(
    object = object,
    con = con
)
print(out)
AcidBase::unlink2(con)

acidgenomics/acidgsea documentation built on Oct. 5, 2023, 7:35 p.m.