newGOM: Constructor for the GeneOverlapMatrix class

In GeneOverlap: Test and visualize gene overlaps

Description

Use this function to create objects of the GeneOverlapMatrix class.

Usage

newGOM(gsetA, gsetB=list(), genome.size=NULL, 
    spec=c('mm9.gene', 'hg19.gene', 'rn4.gene'))

Arguments

gsetA	Gene set A as a named list with each element being a vector/factor of gene names.
gsetB	Gene set B as a named list with each element being a vector/factor of gene names.
genome.size	The number of genes in the genome as an integer.
spec	A string description of the genome to use. There are a few presetted genome sizes to choose from for a user's convenience.

Details

This will create a matrix so that each grid represents the comparison between the two gene lists from the two gene sets. Given two gene sets A and B, the matrix will represent all comparisons bewteen gene lists in A vs. gene lists in B. The set A will be shown as rows and the set B will be shown as columns. If only gene set A is given, the matrix will represent all comparisons between gene lists within the gene set and only the upper triangular matrix will be used.

Value

A GeneOverlapMatrix object. Use accesssors to access to its internal structure and members. Use show or print to obtain summarized information. Use drawHeatmap to visualize it.

See Also

GeneOverlapMatrix-class, GeneOverlap-class

Examples

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

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