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GO Slim Summary

Source: R/goSlimSummary.R
goSlimSummary.Rd

Outputs a brief summary of input genes based on GO Slim data.

Usage

goSlimSummary(
  organism = "hsapiens",
  geneList,
  outputFile,
  outputType = "pdf",
  isOutput = TRUE,
  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.

geneList

A list of input genes.

outputFile

Output file name.

outputType

File format of the plot: pdf, bmp or png.

isOutput

Boolean if a plot is save to outputFile.

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 the summary result.