Description Objects from the Class Slots Methods Details Note Author(s) See Also Examples
This stores the actual gene lists and related information that will be used in categoryCompare.
Objects can be created by calls of the form new("ccGeneList", list))
. ccGeneList
is actually just an extension of R list objects. The input list
should be a list of lists. See Details
for more information.
fdr
:Object of class "numeric"
The number of fdr
runs to perform to account for different list sizes and term dependence
pvalueCutoff
:Object of class "numeric"
Value used to determine whether or not a particular term is significant or not
ccType
:Object of class "character"
What types of annotations to use. Currently supported ones include "BP", "MF", "CC" (from Gene Ontology) and "KEGG"
testDirection
:Object of class "character"
Are you interested in "over" or "under" represented annotations
signature(object = "ccGeneList")
: how many random runs to perform
signature(object = "ccGeneList")
: change the number of random runs
signature(object = "ccGeneList")
: what is the pvalue to consider significant
signature(object = "ccGeneList")
: change the cutoff for significance
signature(object = "ccGeneList")
: what type of annotations are going to be examined
signature(object = "ccGeneList")
: change the type of annotations to examine
signature(object = "ccGeneList")
: query for "over" or "under" represented annotations
signature(object = "ccGeneList")
: change the type of representation ("over" or "under")
signature(object = "ccGeneList")
: what are the names of the lists contained
The input list should be a list of lists, with at least three sub-lists.
testList <- list(list1=list(genes='...',universe='...',annotation='...'), list2=list(...))
: These are the gene identifiers of the genes that are of interest (differentially expressed genes)
: All of the genes that were measured in this particular experiments (i.e. all the genes on the chip)
: What organism or chip do these ID's come from (e.g. "org.Hs.eg.db" for Human Entrez gene ID's, "hgu133a.db" for probe ID's from the Affymetrix U133A chip)
: A data-frame that contains extra information about the genes of interest. At the very least, the data-frame must have a column ID
that matches the ID's contained in genes
What actually happens when running ccEnrich
is that the appropriate HyperGParamsCC
objects are generated for each geneList and each type of annotation (e.g. BP, CC, KEGG), and then the calculations performed on each one.
The ccGeneList
object is what will undergo all of the enrichment calculations. When the results are combined with the ccOptions
object, we can get our results of actual comparisons between experiments.
Robert M Flight
1 2 3 4 5 6 7 8 9 10 | data(ccData)
g10 <- (unique(table10$Entrez[1:100]))
g48 <- (unique(table48$Entrez[1:100]))
list10 <- list(genes=g10, universe=gUniverse, annotation="org.Hs.eg.db")
list48 <- list(genes=g48, universe=gUniverse, annotation="org.Hs.eg.db")
geneLists <- list(T10=list10, T48=list48)
geneLists <- new("ccGeneList", geneLists, ccType=c("BP","KEGG"))
geneLists
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.