In Bioconductor/SOUNDBoard: Statistically-informed Multi-Omics Reports for Tumor and Other Boards

knitr::opts_chunk$set(echo = TRUE)
suppressPackageStartupMessages({
    library(SOUNDBoard)
    library(shiny)
})

suppressMessages({
    x <- SOUNDManager(getwd())
})

Board and case summary

tbl(x, "board") %>% 
    filter(board_uid == "GBMset") %>% 
    sbreport()

tbl(x, "cases") %>% filter(case_uid == "TCGA-32-2615") %>%
    select(-board_uid) %>% sbreport()

GISTIC Score and Thresholded by Gene

tbl(x, "assay") %>%
    filter(case_uid == "TCGA-32-2615", assay == "GISTIC2") %>%
    sbreport()

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