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

In GeneOverlap: 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]>

Lab:http://shenlab-sinai.github.io/shenlab-sinai/

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)

Example output

A <4 x 3> GeneOverlapMatrix object
Geneset A sizes:
 H3K4me3  H3K9me3 H3K27me3 H3K36me3 
   13448      297     3853     4533 
Geneset B sizes:
  Exp High Exp Medium    Exp Low 
      6540       6011       8684 
A GeneOverlapMatrix object:
###### Intersection ######
         Exp High Exp Medium Exp Low
H3K4me3      5916       4985    2583
H3K9me3        66        142      90
H3K27me3      574       1549    1745
H3K36me3     3290       1151     101
###### P-value ######
          Exp High   Exp Medium      Exp Low
H3K4me3  0.0000000 0.000000e+00 1.000000e+00
H3K9me3  0.9996654 7.071538e-13 9.999497e-01
H3K27me3 1.0000000 2.797009e-69 1.061420e-09
H3K36me3 0.0000000 9.999998e-01 1.000000e+00
###### Odds Ratio ######
           Exp High Exp Medium    Exp Low
H3K4me3   8.9672775  3.8589147 0.06418943
H3K9me3   0.6366248  2.3460391 0.62254173
H3K27me3  0.3338513  1.9408115 1.24113618
H3K36me3 10.9219512  0.8265542 0.02145576
###### Jaccard Index ######
            Exp High Exp Medium     Exp Low
H3K4me3  0.420409323 0.34441067 0.132129521
H3K9me3  0.009747452 0.02302952 0.010122596
H3K27me3 0.058458091 0.18628984 0.161693847
H3K36me3 0.422716176 0.12253806 0.007700518

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