gokeggLister {compdiagTools} | R Documentation |
Uses hypergeometric tests to evaluate overrepresentation of KEGG pathway and GO annotations in gene lists.
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)
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. |
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.
A string containing HTML code to be added on an HTML page.
Claudio Lottaz <lottaz@molgen.mpg.de>
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)