In GENE.E: Interact with GENE-E from R

library(knitr)
options(width=80)

hook_output = knit_hooks$get('output')
knit_hooks$set(output = function(x, options) {
  # this hook is used only when the linewidth option is not NULL
  if (!is.null(n <- options$linewidth)) {
    x = knitr:::split_lines(x)
    # any lines wider than n should be wrapped
    if (any(nchar(x) > n)) x = strwrap(x, width = n)
    x = paste(x, collapse = '\n')
  }
  hook_output(x, options)
})

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) 

suppressPackageStartupMessages(library(GENE.E))
suppressPackageStartupMessages(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)))))

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()

GENE.E documentation built on May 31, 2017, 3:11 p.m.