getReadonlyMatrix: Read-only accessors for the various slots of the...

In GeneOverlap: Test and visualize gene overlaps

Description

The gsetA and gsetB slots contain the gene set A and B as named lists. The self.compare slot contains the Boolean label for whether self-comparison is performed. Use getMatrix to retrieve intersection, union, Jaccard index, p-value and odds ratio as a matrix. Use getNestedList to retrieve the intersection and union gene lists and contingency tables as a nested list (outer list represents columns and inner list represents rows). Use brackets [] to retrieve a particular GeneOverlap object within the GeneOverlapMatrix object.

Usage

## S4 method for signature 'GeneOverlapMatrix'
getGsetA(object)
## S4 method for signature 'GeneOverlapMatrix'
getGsetB(object)
## S4 method for signature 'GeneOverlapMatrix'
getSelfCompare(object)
## S4 method for signature 'GeneOverlapMatrix'
getMatrix(object, name=c("pval", 
    "odds.ratio", "intersection", "union", "Jaccard"))
## S4 method for signature 'GeneOverlapMatrix'
getNestedList(object, name=c(
    "intersection", "union", "cont.tbl"))
## S4 method for signature 'GeneOverlapMatrix'
x[i, j]

Arguments

object	A GeneOverlapMatrix object.
x	A GeneOverlapMatrix object.
name	A string description of the information to retrive. Use pval and odds.ratio to retrieve p-values and odds ratios. Use Jaccard to retrieve Jaccard indices. In the context of matrix retrieval, intersection and union will return the numbers of genes. While in the case of nested list retrieval, intersection and union will return the actual gene lists. Use cont.tbl to retrieve the contingency tables.
i, j	Integer or character indices to retrieve GeneOverlap objects from the matrix.

Details

When character indices are used, they should match the names of gsetA or gsetB.

See Also

GeneOverlapMatrix-class

Examples

data(GeneOverlap)
gom.obj <- newGOM(hESC.ChIPSeq.list, hESC.RNASeq.list, gs.RNASeq)
getMatrix(gom.obj, "odds.ratio")
inter.nl <- getNestedList(gom.obj, "intersection")
str(inter.nl)
go.k4.high <- gom.obj[1, 1]
go.k4.high

GeneOverlap documentation built on Nov. 8, 2020, 5:46 p.m.