geneLister {compdiagTools}R Documentation

geneLister - tool for pretty gene listing

Description

This function annotates a given set of probe ids. It generates either a string representing a HTML table or plain text. In the plain text version the probes are sperated by \n and each annotation is seperated by the given 'sep' character.\ Note: To use CORG annotations, the 'CorgAnn' package must be available. If a twilight object is given, the resulting list is ordered by qvalue and observed test statistic.

Usage

geneLister(obj, chip=NULL, hc="#99CCCC",
           bgc1="#CCCCCC", bgc2="#E8E8E8", HTML = TRUE,
           info = NULL, annotCORG = FALSE, annotLOCUS = TRUE,
           annotGO = TRUE, annotSYMBOL = TRUE,
           annotGDESCRIPTION = TRUE, annotPROBE = TRUE,
           annotUNIGENE   = TRUE, annotGENBANK = TRUE,
           annotLOCUSLINK = TRUE,annotPUBMED = TRUE,
           annotKEGG = TRUE, annotOMIM = TRUE,
           annotGENECARDS = TRUE,sep = "\t",
           verbose = FALSE, maxfdr=1, maxgenes=500,
           lookupProbes=NULL, groupname = "n/a", links = FALSE)

Arguments

obj Either a geneList object, a twilight object or a vector of probe ids
chip Character string specifying used chip. Only necessary, if obj is not an geneList object.
info Vector of character strings. Specifying the names of data.frame columns that should be included into the annotation. Works only for geneLists objects, which have a named data.frame in 'geneInfos' slot.
HTML Logical value switching between HTML and TEXT mode
hc Character string denoting background color for table head
bgc1 Character string denoting 1st background color for a table row
bgc2 Character string denoting 2nd background color for a table row
sep Character string to seperate items (used only in non HTML mode)
verbose Logical value for message printing
annotCORG Logical value denoting inclusion of CORG annotations
annotLOCUS Logical value denoting inclusion of chromosomal location
annotGO Logical value denoting inclusion of GO annotations
annotSYMBOL Logical value denoting inclusion of gene symbol annotations
annotGDESCRIPTION Logical value denoting inclusion of gene description
annotPROBE Logical value denoting inclusion of PROBE ID annotations
annotUNIGENE Logical value denoting inclusion of UNIGENE annotations
annotGENBANK Logical value denoting inclusion of GENBANK annotations
annotLOCUSLINK Logical value denoting inclusion of LOCUSLINK annotations
annotPUBMED Logical value denoting inclusion of PUBMED annotations
annotKEGG Logical value denoting inclusion of KEGG annotations
annotOMIM Logical value denoting inclusion of OMIM annotations
annotGENECARDS Logical value denoting inclusion of GENECARDS annotations
maxfdr Only probes with qvalue <maxfdr are listed. (!only considered if twilight object is given!)
maxgenes Maximal number of genes in list. (!only considered if twilight object is given!)
lookupProbes probe identifiers used for looking up annotations, may differ from probe identifiers shown in the table.
groupname Specifies the name of the group, where the shown gene came from.
links Flags if the symbol annotation should include a link on the affy-id in the genelist. This feature was added support the navigation from the GO graph of the gokeggLister to the Symbol Ids of the geneLister.

Value

return A character string representing either a HTML table or plain text seperated by 't'.

Author(s)

M. Held

Examples

library(hgu95av2)
ids <- ls(hgu95av2GO)[1:20]
geneLister(ids, chip="hgu95av2")

[Package compdiagTools version 1.5.3 Index]