idMapping: 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/"
)

Value

A list of mapped and unmapped IDs.

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.