changeIds {SBGNview} | R Documentation

## Change input IDs to another ID type

### Description

Change input IDs to another ID type

### Usage

    changeIds(input.ids, input.type, output.type, cpd.or.gene,
      limit.to.pathways = NULL, org = "hsa",
      SBGNview.data.folder = "./SBGNview.tmp.data")

### Arguments

`input.ids` | A vector of character strings. Input IDs that need to be converted.
`input.type` | A character string. The type of input IDs. Supported ID types can be found in data(mapped.ids)
`output.type` | A character string. The type of output IDs. Supported ID types can be found in data(mapped.ids)
`cpd.or.gene` | A character string. One of "gene" or "compound". Currently only supports macromolecule and simple chemical IDs. This parameter is used to find the ID mapping between input node set IDs and glyph IDs.
`limit.to.pathways` | A vector of character strings. A vector of pathways IDs. When *output.type* is one of "pathwayCommons" or "metacyc.SBGN", one input ID(e.g. gene symbol) can map to multiple nodes in different pathways (SBGN-ML files). In this case, we can limit output to the specified pathways. When *output.type* is NOT one of "pathwayCommons" or "metacyc.SBGN", this argument is ignored.
`org` | Character string. Three letter KEGG species code.
`SBGNview.data.folder` | A character string. The path to a folder that will hold download ID mapping files and pathway information data files. The data can be reused once downloaded.

### Value

A list. Each element is the IDs in output.type that are mapped to one input ID.

### Examples

     data(mapped.ids)
    mapping = changeIds(
      input.ids = c(100048912),
      input.type = "ENTREZID",
      output.type = "pathwayCommons",
      cpd.or.gene = "gene",
    )

[Package SBGNview version 1.0.0 Index]