## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set( collapse=TRUE, comment="#>", warning=FALSE, message=FALSE ) ## ----eval=FALSE--------------------------------------------------------------- # ## Install the development version from GitHub # devtools::install_github("dpique/receptLoss", # build_opts=c("--no-resave-data", "--no-manual"), # build_vignettes=TRUE) ## ----warning=FALSE, message=FALSE--------------------------------------------- library(receptLoss) library(dplyr) library(ggplot2) set.seed(100) ## Simulate matrix of expression values from ## 10 genes measured in both normal tissue and ## tumor tissue in 100 patients exprMatrNml <- matrix(abs(rnorm(100, mean=2.5)), nrow=10) exprMatrTum <- matrix(abs(rnorm(1000)), nrow=10) geneNames <- paste0(letters[seq_len(nrow(exprMatrNml))], seq_len(nrow(exprMatrNml))) rownames(exprMatrNml) <- rownames(exprMatrTum) <- geneNames ## ----------------------------------------------------------------------------- nSdBelow <- 2 minPropPerGroup <- .2 rl <- receptLoss(exprMatrNml, exprMatrTum, nSdBelow, minPropPerGroup) head(rl) ## ----------------------------------------------------------------------------- clrs <- c("#E78AC3", "#8DA0CB") tryCatch({plotReceptLoss(exprMatrNml, exprMatrTum, rl, geneName=as.character(rl[1,1]), clrs=clrs)}, warning=function(cond){ knitr::include_graphics("rl_fig.png") }, error=function(cond){ knitr::include_graphics("rl_fig.png") } ) ## ----------------------------------------------------------------------------- receptLoss::nhrs ## ----eval=FALSE--------------------------------------------------------------- # vignette("receptLoss") ## ----------------------------------------------------------------------------- sessionInfo()