Import and export

The functions import and export load and save objects from and to particular file formats. The unisets package aims to implement support for a number of annotation and sequence formats. The following file formats are currently supported: GMT.

GMTFile(resource)

import.gmt(con, ...)

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

export.gmt(object, con, ...)

# S4 method for Sets,GMTFile,ANY
export(object, con, format, ...)

import.Go3AnnDbBimap(con, format, text, ...)

# S4 method for Go3AnnDbBimap,ANY,ANY
import(con, format, text, ...)

Arguments

resource	For GMTFile(), the .gmt file that will be imported in.
con	The connection from which data is loaded or to which data is saved. If this is a character vector, it is assumed to be a filename and a corresponding file connection is created and then closed after exporting the object. If a RTLFile derivative, the data is loaded from or saved to the underlying resource. Certain subclasses of BiMap are supported: Go3AnnDbBimap.
...	Parameters to pass to the format-specific method.
format, text	Arguments defined in the rtracklayer::import() generic. Currently ignored.
object	An object of class inheriting from GMTFile.
Go3AnnDbBimap	A Go3AnnDbBimap.

Value

For GMTFile(), an object representing the path to a .gmt file on disk

Coercion to Sets

as(Go3AnnDbBimap, "Sets") and as.Sets(Go3AnnDbBimap) return a Sets from a Gene Ontology Bimap stored distributed in a Bioconductor annotation package.

Examples

# Example file ----

gmt <- system.file(package="unisets", "extdata", "example.gmt")

# Import ----

bs <- import(gmt)
bs
#> Sets with 674 relations between 633 elements and 4 sets
#>           element                              set
#>       <character>                      <character>
#>   [1]        JUNB HALLMARK_TNFA_SIGNALING_VIA_NFKB
#>   [2]       CXCL2 HALLMARK_TNFA_SIGNALING_VIA_NFKB
#>   [3]        ATF3 HALLMARK_TNFA_SIGNALING_VIA_NFKB
#>   [4]      NFKBIA HALLMARK_TNFA_SIGNALING_VIA_NFKB
#>   [5]     TNFAIP3 HALLMARK_TNFA_SIGNALING_VIA_NFKB
#>   ...         ...                              ...
#> [670]      STK38L         HALLMARK_MITOTIC_SPINDLE
#> [671]       YWHAE         HALLMARK_MITOTIC_SPINDLE
#> [672]     RAPGEF5         HALLMARK_MITOTIC_SPINDLE
#> [673]       CEP72         HALLMARK_MITOTIC_SPINDLE
#> [674]      CSNK1D         HALLMARK_MITOTIC_SPINDLE
#> -----------
#> elementInfo: IdVector with 0 metadata
#>     setInfo: IdVector with 1 metadata (source)

# Export ----

tf <- tempfile(fileext = ".gmt")
export(bs, tf)

# Import (Go3AnnDbBimap) ----

library(org.Hs.eg.db)
bs1 <- import(org.Hs.egGO)
#> 'select()' returned 1:1 mapping between keys and columns
#> Coercing evidence to factor
#> Coercing ontology to factor
bs1
#> GOSets with 322301 relations between 20488 elements and 18177 sets
#>              element         set | evidence ontology
#>          <character> <character> | <factor> <factor>
#>      [1]           1  GO:0002576 |      TAS       BP
#>      [2]           1  GO:0008150 |      ND        BP
#>      [3]           1  GO:0043312 |      TAS       BP
#>      [4]           2  GO:0001869 |      IDA       BP
#>      [5]           2  GO:0002576 |      TAS       BP
#>      ...         ...         ... .      ...      ...
#> [322297]   111089941  GO:0004571 |      IMP       MF
#> [322298]   111089941  GO:0005509 |      IEA       MF
#> [322299]   111240474  GO:0005515 |      IPI       MF
#> [322300]   112441434  GO:0005515 |      IPI       MF
#> [322301]   113219467  GO:0030533 |      IEA       MF
#> -----------
#> elementInfo: EntrezIdVector with 0 metadata
#>     setInfo: GOIdVector with 4 metadata (GOID, DEFINITION, ...)