gokeggLister {compdiagTools}R Documentation

Evaluate Overrepresentation of GO Terms and Pathways in Gene Lists

Description

Uses hypergeometric tests to evaluate overrepresentation of KEGG pathway and GO annotations in gene lists.

Usage

gokeggLister(x, chip, groupname="first group", ngenes = NULL, max.q = NULL,
             gomf = TRUE, gobp = TRUE, gocc = TRUE, kegg = TRUE, 
             outputPath = ".", max.p = 0.01, links = FALSE, legend = FALSE, 
             allChipLLs=NULL, is.upreg=NULL, bw.colors=FALSE, fontpath=NULL)

Arguments

x a vector of probe-set identifiers as character strings or a twilight object if allChipLLs is NULL. Otherwise x is expected to contain numeric LocusLink identifiers
chip a character string giving the name of a chip, i.e. its annotation library. This is an Affymetrix chip name if allChipLLs is null and one of humanLLMappings, mouseLLMappings or ratLLMappings otherwise.
groupname Specifies the name of the group, where the genes used for the analysis came from.
ngenes number of genes taken into account
max.q take all genes with q-values lower than max.q into account. Only valid when x is a twilight object.
gomf logical, TRUE if the molecular function branch of GO is to be evaluated.
gobp logical, TRUE if the biological process branch of GO is to be evaluated.
gocc logical, TRUE if the cellular component branch of GO is to be evaluated.
kegg logical, TRUE if the KEGG pathways are to be evaluated.
outputPath where to store the bitmaps for graphs
max.p numerical, defines the maximal p-value tolerated for GO/KEGG nodes considered as overrepresented
links Flags if external link sites for every GO graph node should be created.
legend Flags if external legend site for the GO graphs should be created.
allChipLLs is NULL if x is a list of probe-sets from an Affymetrix chip. For other microarrays, this is a complete list of numeric LocusLink identifiers for all reporters.
is.upreg for each element of x contains a logical value specifying whether the corresponding probe-set/reporter is up regulated in groupname.
bw.colors If FALSE up- and down-regulation overrepresentation is represented in graphs by shades of red and green (default). If set to TRUE, this is shown using different shapes of nodes.
fontpath is used by 'dot' to get fonts for the drawing of graphs. The default (NULL) tries to guess in a few standard paths.

Details

Hypergeometric tests are performed for each GO term of selected branches and for all KEGG pathways if required. These tests compute p-values to evaluate the likelyhood that the corresponding number of annotations is occurring in a random list of genes of the same size.

If upreg is specified, the analysis is carried out separately for up and down regulated probe-sets/reporters. For twilight objects gokeggLister determines automatically which probe-sets/reporters are up or down regulated.

Value

A string containing HTML code to be added on an HTML page.

Author(s)

Claudio Lottaz <lottaz@molgen.mpg.de>

Examples

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

llids=unique(unlist(mget(ids,env=hgu95av2LOCUSID)))
allLLids=unique(unlist(as.list(hgu95av2LOCUSID)))
gokeggLister(llids, chip="humanLLMappings", outputPath=NULL, allChipLLs=allLLids)

library(humanLLMappings)
ids <- ls(humanLLMappingsLL2GO)[1:100]
all.ids <- ls(humanLLMappingsLL2GO)[1:1000]
gokeggLister(ids, chip="humanLLMappings", allChipLLs=all.ids)

[Package compdiagTools version 1.5.3 Index]