## ----eval=FALSE, echo=TRUE---------------------------------------------------- # if (!require('PDATK')) BiocManager::install('PDATK') ## ----load_package------------------------------------------------------------- library(PDATK) ## ----SurvivalExperiment_constructor------------------------------------------- # -- Create some dummy data # an assay assay1 <- matrix(rnorm(100), nrow=10, ncol=10, dimnames=list(paste0('gene_', seq_len(10)), paste0('sample_', seq_len(10)))) # column and row metadata rowMData <- DataFrame(gene_name=rownames(assay1), id=seq_len(10), row.names=rownames(assay1)) colMData <- DataFrame(sample_name=colnames(assay1), overall_survival=sample.int(1000, 10), os_status=sample(c(0L, 1L), 10, replace=TRUE), row.names=colnames(assay1)) # -- Use it to build a SurvivalExperiment survExperiment <- SurvivalExperiment(assays=SimpleList(rna=assay1), rowData=rowMData, colData=colMData, metadata=list(a='Some metadata'), survival_time='overall_survival', event_occurred ='os_status') ## ----------------------------------------------------------------------------- # -- Build A SummarizedExperiment sumExperiment <- SummarizedExperiment(assays=SimpleList(rna=assay1), rowData=rowMData, colData=colMData, metadata=list(a='Some meta data')) # -- Convert it to a SurvivalExperiment # Use the sumExp parameter, which must be named survExperiment <- SurvivalExperiment(sumExp=sumExperiment, survival_time='overall_survival', event_occurred='os_status') ## ----CohortList_constructor--------------------------------------------------- cohortList <- CohortList(list(cohort1=survExperiment, cohort2=survExperiment), mDataTypes=c('rna_seq', 'rna_micro')) ## ----SurvivalModel_constructor------------------------------------------------ set.seed(1987) survModel <- SurvivalModel(survExperiment, randomSeed=1987)