## ----echo=FALSE--------------------------------------------------------------- CRANpkg <- function (pkg) { cran <- "https://CRAN.R-project.org/package" fmt <- "[%s](%s=%s)" sprintf(fmt, pkg, cran, pkg) } Biocpkg <- function (pkg) { sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg) } ## ----getPackage, eval=FALSE--------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("CrossICC") ## ----getDevel, eval=FALSE----------------------------------------------------- # BiocManager::install("bioinformatist/CrossICC") ## ----Load, message=FALSE, eval = TRUE----------------------------------------- library(CrossICC) ## ----------------------------------------------------------------------------- library(CrossICC) data(demo.platforms) # Turn on use.shiny parameter if you want to call shiny once the CrossICC finished CrossICC.object <- CrossICC(demo.platforms, skip.mfs = TRUE, use.shiny = FALSE, overwrite = TRUE, output.dir = tempdir()) ## ----------------------------------------------------------------------------- Mcluster <- paste("K", CrossICC.object$clusters$clusters[[1]], sep = "") CrossICC.ssGSEA <- ssGSEA(x = demo.platforms[[1]], gene.signature = CrossICC.object$gene.signature, geneset2gene = CrossICC.object$unioned.genesets, cluster = Mcluster) ## ----------------------------------------------------------------------------- predicted <- predictor(demo.platforms[[1]], CrossICC.object) ## ----------------------------------------------------------------------------- sessionInfo()