knitr::opts_chunk$set(echo = TRUE, cache = TRUE)
suppressPackageStartupMessages({
    library(SOUNDBoard)
    library(S4Vectors)
    library(curatedTCGAData)
    library(DT)
    library(shiny)
})

Load packages

    library(SOUNDBoard)
    library(S4Vectors)
    library(curatedTCGAData)
    library(DT)
    library(shiny)

Data Setup

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"))

SOUNDBoard Setup

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])
    )
}

Embedded Application

sbreport(SOUNDBoardWidget(x))


Bioconductor/SOUNDBoard documentation built on May 6, 2019, 7:52 a.m.