Description Usage Arguments Details Value Author(s) Examples
Function to get and set configuration parameters determining the default behavior of the EnrichmentBrowser
1 | configEBrowser(key, value = NULL)
|
key |
Configuration parameter. |
value |
Value to overwrite the current value of key. |
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)
If is.null(value) this returns the value of the selected configuration parameter. Otherwise, it updates the selected parameter with the given value.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
1 2 3 4 5 6 7 8 9 10 | # 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()
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