knitr::opts_chunk$set(echo = TRUE, cache = TRUE)
suppressPackageStartupMessages({ library(SOUNDBoard) library(S4Vectors) library(curatedTCGAData) library(DT) library(shiny) })
library(SOUNDBoard) library(S4Vectors) library(curatedTCGAData) library(DT) library(shiny)
suppressMessages({ gbm <- curatedTCGAData("GBM", c("GISTICT", "GISTICA", "RNASeq2GeneNorm"), FALSE) }) ## Extract Hugo_Symbols column rownames(gbm[[3]]) <- RaggedExperiment::mcols(gbm[[3]])[["Hugo_Symbol"]] genesOfInterest <- c("FAF1", "ASTN1", "PROX1", "PARP1", "AKR1C4", "TAF3") suppressMessages({ gbm <- gbm[genesOfInterest, 1:3, ] }) GBM_colData <- colData(gbm) GBM_colData <- GBM_colData[, c("Age..years.at.diagnosis.", "gender", "tumor_tissue_site", "race")] names(GBM_colData)[1:3] <- c("age", "sex", "primary_site") GBM_colData <- c(DataFrame(board_uid = "GBMset", case_uid = rownames(GBM_colData)), GBM_colData, DataFrame(diagnosis = "GBM")) GBM_GISTIC <- as.data.frame(assay(gbm[[1L]])) suppressMessages({ ov <- curatedTCGAData("OV", "CN*", FALSE) ov <- ov[1:5, 1:3, ] }) ov_coldata <- colData(ov) ov_coldata <- ov_coldata[, c("patient.age_at_initial_pathologic_diagnosis", "gender", "tumor_tissue_site", "patient.race")] names(ov_coldata) <- c("age", "sex", "primary_site", "race") ov_coldata <- c(DataFrame(board_uid = "OVset", case_uid = rownames(ov_coldata)), ov_coldata, DataFrame(diagnosis = "OV")) OV_CGH_415 <- as.data.frame(assay(ov[[2L]], "Segment_Mean"))
x <- SOUNDManager(tempfile(), "../inst/template/KBoard.sql", "../inst/template/SOUNDClinical.Rmd") tbl(x, "board") <- list( board_uid = "GBMset", description = "Clinical management of GlioBlastoma Multiforme" ) tbl(x, "board") <- list( board_uid = "OVset", description = "Ovarian Cancer Klinischer Management" ) tbl(x, "cases") <- GBM_colData tbl(x, "cases") <- ov_coldata gbrows <- seq_len(nrow(GBM_colData)) for (i in gbrows) { tbl(x, "assay") <- list( case_uid = GBM_colData[i, "case_uid"], assay = "GISTIC2", description = paste("GISTIC_DATA", i), resource = manage(x, GBM_GISTIC[, i, drop = FALSE]) ) } ovrows <- seq_len(nrow(ov_coldata)) for (i in ovrows) { tbl(x, "assay") <- list( case_uid = ov_coldata[i, "case_uid"], assay = "CGH_415K", description = paste("CGH_Data", i), resource = manage(x, OV_CGH_415[, i, drop = FALSE]) ) }
sbreport(SOUNDBoardWidget(x))
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