EnrichmentBrowser (version 2.2.2)

config.ebrowser: Configuring the EnrichmentBrowser

Description

Function to get and set configuration parameters determining the default behavior of the EnrichmentBrowser

Usage

config.ebrowser( key, value = NULL )

Arguments

key

Configuration parameter.

value

Value to overwrite the current value of key.

Value

If is.null(value) this returns the value of the selected configuration parameter. Otherwise, it updates the selected parameter with the given value.

Details

Important pData, fData, and result column names:

• SMPL.COL: pData column storing the sample IDs (default: "SAMPLE")
• GRP.COL: pData column storing binary group assignment (default: "GROUP")
• BLK.COL: pData column defining paired samples or sample blocks (default: "BLOCK")

• PRB.COL: fData column storing probe/feature IDs ("PROBEID", read-only)
• EZ.COL: fData column storing gene ENTREZ IDs ("ENTREZID", read-only)
• SYM.COL: fData column storing gene symbols ("SYMBOL", read-only)
• GN.COL: fData column storing gene names ("GENENAME", read-only)

• FC.COL: fData column storing (log2) fold changes of differential expression between sample groups (default: "FC")
• ADJP.COL: fData column storing adjusted (corrected for multiple testing) p-values of differential expression between sample groups (default: "ADJ.PVAL")

• GS.COL: result table column storing gene set IDs (default: "GENE.SET")
• GSP.COL: result table column storing gene set significance (default: "P.VALUE")
• PMID.COL: gene table column storing PUBMED IDs ("PUBMED", read-only)

Important URLs (all read-only):

• NCBI.URL: http://www.ncbi.nlm.nih.gov/
• PUBMED.URL: http://www.ncbi.nlm.nih.gov/pubmed/
• GENE.URL: http://www.ncbi.nlm.nih.gov/gene/
• KEGG.URL: http://www.genome.jp/dbget-bin/
• KEGG.GENE.URL: http://www.genome.jp/dbget-bin/www_bget?
• KEGG.SHOW.URL: http://www.genome.jp/dbget-bin/show_pathway?
• GO.SHOW.URL: http://amigo.geneontology.org/amigo/term/

Default output directory:

• EBROWSER.HOME: system.file(package="EnrichmentBrowser")
• OUTDIR.DEFAULT: file.path(EBROWSER.HOME, "results")

Gene set size:

• GS.MIN.SIZE: minimum number of genes per gene set (default: 5)
• GS.MAX.SIZE: maximum number of genes per gene set (default: 500)

Result appearance:

• RESULT.TITLE: (default: "Table of Results")
• NR.SHOW: maximum number of entries to show (default: 20)

Examples

    # getting config information
    config.ebrowser("GS.MIN.SIZE") 

    # setting config information
    # WARNING: this is for advanced users only!
    # inappropriate settings will impair EnrichmentBrowser's functionality
    config.ebrowser(key="GS.MIN.SIZE", value=3)