GENE.E

The GENE.E package provides the ability to transfer matrices, dendrograms, and annotations between R and GENE-E. Two methods are provided:

• from.genee Gets the current selection from GENE-E.
• to.genee Sends a matrix and annotations to GENE-E.

Example Usage

For illustration of GENE.E usage, we use the Golub et al. data set on acute leukemia from the golubEsets package. First, load the GENE.E and golubEsets packages:

library(GENE.E)
library(golubEsets) 

Next, ensure that GENE-E is running and then issue the following commands to load the data and send the data to GENE-E:

data(Golub_Merge) 
to.genee(exprs(Golub_Merge), fData(Golub_Merge), show.colnames=F, pData(Golub_Merge)[,c('Gender', 'ALL.AML')], column.hclust=hclust(dist(t(exprs(Golub_Merge)))))

## Warning in is(h5id, "H5IdComponent"): restarting interrupted promise evaluation

In GENE-E, (see video below), drag the dotted line to cut the sample dendrogram. Next, click a dendrogram branch to select the samples in that branch.

Finally, get the selected data in GENE-E back into our R session:

Sys.sleep(5)
selection <- from.genee()