## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------ library(MultiAssayExperiment) library(S4Vectors) ## ----------------------------------------------------------------------------- data(miniACC) miniACC ## ----------------------------------------------------------------------------- colData(miniACC)[1:4, 1:4] table(miniACC$race) ## ----------------------------------------------------------------------------- experiments(miniACC) ## ----------------------------------------------------------------------------- sampleMap(miniACC) ## ----------------------------------------------------------------------------- metadata(miniACC) ## ----results='hide'----------------------------------------------------------- miniACC[c("MAPK14", "IGFBP2"), , ] ## ----results='hide'----------------------------------------------------------- stg4 <- miniACC$pathologic_stage == "stage iv" # remove NA values from vector miniACC[, stg4 & !is.na(stg4), ] ## ----results='hide'----------------------------------------------------------- miniACC[, , "RNASeq2GeneNorm"] ## ----------------------------------------------------------------------------- miniACC[[1L]] #or equivalently, miniACC[["RNASeq2GeneNorm"]] ## ----------------------------------------------------------------------------- summary(complete.cases(miniACC)) ## ----------------------------------------------------------------------------- accmatched = intersectColumns(miniACC) ## ----------------------------------------------------------------------------- colnames(accmatched) ## ----------------------------------------------------------------------------- accmatched2 <- intersectRows(miniACC[, , c("RNASeq2GeneNorm", "gistict", "Mutations")]) rownames(accmatched2) ## ----------------------------------------------------------------------------- class(assay(miniACC)) ## ----------------------------------------------------------------------------- assays(miniACC) ## ----------------------------------------------------------------------------- longFormat(miniACC[c("TP53", "CTNNB1"), , ], colDataCols = c("vital_status", "days_to_death")) ## ----------------------------------------------------------------------------- wideFormat(miniACC[c("TP53", "CTNNB1"), , ], colDataCols = c("vital_status", "days_to_death")) ## ----------------------------------------------------------------------------- MultiAssayExperiment(experiments=experiments(miniACC), colData=colData(miniACC), sampleMap=sampleMap(miniACC), metadata=metadata(miniACC)) ## ----------------------------------------------------------------------------- miniACC2 <- c(miniACC, log2rnaseq = log2(assays(miniACC)$RNASeq2GeneNorm), mapFrom=1L) assays(miniACC2) ## ----------------------------------------------------------------------------- library(UpSetR) upsetSamples(miniACC) ## ----message=FALSE------------------------------------------------------------ library(survival) library(survminer) coldat <- as.data.frame(colData(miniACC)) coldat$y <- Surv(miniACC$days_to_death, miniACC$vital_status) colData(miniACC) <- DataFrame(coldat) ## ----------------------------------------------------------------------------- miniACC <- miniACC[, complete.cases(coldat$y), ] coldat <- as(colData(miniACC), "data.frame") ## ----------------------------------------------------------------------------- fit <- survfit(y ~ pathology_N_stage, data = coldat) ggsurvplot(fit, data = coldat, risk.table = TRUE) ## ----------------------------------------------------------------------------- wideacc <- wideFormat(miniACC["EZH2", , ], colDataCols = c("vital_status", "days_to_death", "pathology_N_stage")) wideacc$y <- Surv(wideacc$days_to_death, wideacc$vital_status) head(wideacc) ## ----------------------------------------------------------------------------- coxph(Surv(days_to_death, vital_status) ~ gistict_EZH2 + log2(RNASeq2GeneNorm_EZH2) + pathology_N_stage, data=wideacc) ## ----------------------------------------------------------------------------- sessionInfo()