```{r setup, echo=FALSE, warn=FALSE} library(knitr) options(width=80) ``` ```{r wrap-hook, echo=FALSE} 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](www.broadinstitute.org/cancer/software/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: ```{r library_GENE.E_fake, eval=FALSE} library(GENE.E) library(golubEsets) ``` ```{r library_GENE.E_real, warn=FALSE, echo=FALSE, results="hide"} 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: ```{r} 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: ```{r} Sys.sleep(5) selection <- from.genee() ```