Description Usage Arguments Details Value See Also Examples
Use this function to create objects of the GeneOverlapMatrix class.
1 2 |
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. |
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.
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.
GeneOverlapMatrix-class
, GeneOverlap-class
1 2 3 4 | data(GeneOverlap)
gom.obj <- newGOM(hESC.ChIPSeq.list, hESC.RNASeq.list, gs.RNASeq)
gom.obj
drawHeatmap(gom.obj)
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