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]