import: Importing/exporting

In Bioconductor/BiocSet: Representing Different Biological Sets

Importing/exporting

Description

Importing/exporting and formating of element sets as a BiocSet object.

Usage

## S4 method for signature 'GMTFile,ANY,ANY'
import(con, format, text, ...)

## S4 method for signature 'BiocSet,GMTFile,ANY'
export(object, con, format, ...)

## S4 method for signature 'OBOFile,ANY,ANY'
import(con, format, text, ...)

## S4 method for signature 'BiocSet,OBOFile,ANY'
export(object, con, format, ...)

Arguments

con	For import, the file name or URL the element set is loaded from. For export, the file name or URL the element set is written to.
format	For import, the format of the input. For export, the format of the output.
text	If con is missing this is a character vector directly providing the element set that should be imported.
...	Parameters to pass to the format-specific method
object	For 'export()', the object to be exported.

Value

For 'import()', a BiocSet object

For 'export()', a GMTFile object representing the location where the BiocSet object was written to

Examples

gmtFile <- system.file(package = "BiocSet", "extdata",
    "hallmark.gene.symbol.gmt")
tbl <- import(gmtFile)

tbl2 <- BiocSet(set1 = letters, set2 = LETTERS)
fl <- tempfile(fileext = ".gmt")
gmt <- export(tbl2, fl)

oboFile <- system.file(package = "BiocSet", "extdata", "sample_go.obo")
tst_obo <- import(oboFile)
fl <- system.file("extdata", "sample_go.obo", package = "BiocSet")
tbl <- import(fl)
new_fl <- tempfile(fileext = ".obo")
obo <- export(tbl, new_fl)

Bioconductor/BiocSet documentation built on Oct. 31, 2024, 11:43 p.m.