GeneOverlapMatrix: Matrix representation of the pairwise overlaps between two...

In shenlab-sinai/geneoverlap-old: Test and visualize gene overlaps

Description

Given one or two gene sets each contains one or more gene lists, create a matrix to represent all pairwise comparisons between the gene lists. This class also provides functions to visualize the matrix.

Usage

## S4 method for signature 'GeneOverlapMatrix'
show(object)
## S4 method for signature 'GeneOverlapMatrix'
print(x, ...)

Arguments

object	A GeneOverlapMatrix object.
x	A GeneOverlapMatrix object.
...	They are not used.

Details

The problem is stated as the representation of all pairwise comparisons between two gene sets each contains one or more gene lists. This is represented as a matrix where the rows correspond to one gene set and the columns correspond to the other. Each grid represents the overlap between two gene lists of the corresponding row and column. This class calls the GeneOverlap constructor to create objects that represent the overlapping information. When there is only one gene set, the matrix represents the self-comparison within the gene set and only the upper triangular matrix is used.

The significance of gene overlap is characterized by two pieces of information: odds ratio and p-value. This class provides functions to visualize these information as a heatmap. The color gradients of each grid represents the odds ratio while the texts superimposed on the grids state the p-values. It is also possible to let the color gradients represent Jaccard index - a measurement of similarity between two sets.

Author(s)

Li Shen <[e-mail]>

Mount Sinai profile:http://www.mountsinai.org/profiles/li-shen

Personal:http://www.linkedin.com/in/lshen/

See Also

GeneOverlap-class

Examples

data(GeneOverlap)
gom.obj <- newGOM(hESC.ChIPSeq.list, hESC.RNASeq.list, gs.RNASeq)
gom.obj
print(gom.obj)
drawHeatmap(gom.obj)

shenlab-sinai/geneoverlap-old documentation built on May 29, 2019, 9:22 p.m.