idMapping {WebGestaltR}

ID Mapping

Description

ID mapping utility with WebGestalt server.

Usage

idMapping(
  organism = "hsapiens",
  dataType = "list",
  inputGeneFile = NULL,
  inputGene = NULL,
  sourceIdType,
  targetIdType = NULL,
  collapseMethod = "mean",
  mappingOutput = FALSE,
  outputFileName = "",
  cache = NULL,
  hostName = "https://www.webgestalt.org/"
)

idToSymbol(
  organism = "hsapiens",
  dataType = "list",
  inputGeneFile = NULL,
  inputGene = NULL,
  sourceIdType = "ensembl_gene_id",
  collapseMethod = "mean",
  mappingOutput = FALSE,
  outputFileName = NULL,
  cache = NULL,
  hostName = "https://www.webgestalt.org/"
)

Arguments

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

dataType

Type of data, either list, rnk or gmt. Could be list, rnk or matrix for idToSymbol.

inputGeneFile

The data file to be mapped.

inputGene

Or the input could be given as an R object. GMT file should be read with readGmt.

sourceIdType

The ID type of the data.

targetIdType

The ID type of the mapped data.

collapseMethod

The method to collapse duplicate IDs with scores. mean, median, min and max represent the mean, median, minimum and maximum of scores for the duplicate IDs.

mappingOutput

Boolean if the mapping output is written to file.

outputFileName

The output file name.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

hostName

The server URL for accessing data. Mostly for development purposes.

Value

A list of mapped and unmapped IDs.