configEBrowser: Configuring the EnrichmentBrowser

In lgeistlinger/EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis

Configuring the EnrichmentBrowser

Description

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

Usage

configEBrowser(key, value = NULL)

Arguments

key	Configuration parameter.
value	Value to overwrite the current value of key.

Details

Important colData, rowData, and result column names:

• SMPL.COL: colData column storing the sample IDs (default: "SAMPLE")

• GRP.COL: colData column storing binary group assignment (default: "GROUP")

• BLK.COL: colData column defining paired samples or sample blocks (default: "BLOCK")

• PRB.COL: rowData column storing probe/feature IDs ("PROBEID", read-only)

• EZ.COL: rowData column storing gene ENTREZ IDs ("ENTREZID", read-only)

• SYM.COL: rowData column storing gene symbols ("SYMBOL", read-only)

• GN.COL: rowData column storing gene names ("GENENAME", read-only)

• FC.COL: rowData column storing (log2) fold changes of differential expression between sample groups (default: "FC")

• ADJP.COL: rowData 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")

• PVAL.COL: result table column storing gene set significance (default: "PVAL")

• 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: tools::R_user_dir("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)

Value

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

Author(s)

Ludwig Geistlinger

Examples

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

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

    # restoring default config settings     
    configEBrowser() 

lgeistlinger/EnrichmentBrowser documentation built on May 9, 2024, 7:22 p.m.