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.Rhistory
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browseVignettes("TCGAbiolinks")
packageVersion("TCGAbiolinks")
library(TCGAbiolinks)
library(dplyr)
library(DT)
query <- GDCquery(
project = "TCGA-GBM",
data.category = "Gene expression",
data.type = "Gene expression quantification",
platform = "Illumina HiSeq",
file.type = "normalized_results",
experimental.strategy = "RNA-Seq",
barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
legacy = TRUE
)
GDCdownload(query, method = "api", files.per.chunk = 10)
data <- GDCprepare(query)
datatable(as.data.frame(colData(data)),
options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
rownames = FALSE)
View(data)
colData(data)
data.colData
query <- GDCquery(
project = "TCGA-GBM",
data.category = "Gene expression",
data.type = "Gene expression quantification",
platform = "Illumina HiSeq",
file.type = "normalized_results",
experimental.strategy = "RNA-Seq",
barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
legacy = TRUE
)
GDCdownload(query, method = "api", files.per.chunk = 10)
data <- GDCprepare(query)
datatable(as.data.frame(colData(data)),
options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
rownames = FALSE)
colnames(colData(data))
data
data$colData
colData[data]
data[colData]
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SummarizedExperiment")
a
datatable(as.data.frame(colData(data)),
options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
rownames = FALSE)
library(SummarizedExperiment)
query <- GDCquery(
project = "TCGA-GBM",
data.category = "Gene expression",
data.type = "Gene expression quantification",
platform = "Illumina HiSeq",
file.type = "normalized_results",
experimental.strategy = "RNA-Seq",
barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
legacy = TRUE
)
GDCdownload(query, method = "api", files.per.chunk = 10)
data <- GDCprepare(query)
data
datatable(as.data.frame(colData(data)),
options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
rownames = FALSE)