Question: Download TCGA dataset like a S4 object
0
gravatar for Giuseppe
15 months ago by
Giuseppe20
Giuseppe20 wrote:

Hi all,

I'm making a function that uses input TCGA datasets. I know that for the purpose of reproducibility, inputs need to be BioC objects, and not text files.

My question is: is there any package that allows me download TCGA datasets like a BioC objects (S4) ?

Thank you so much!

tcga dataset • 380 views
ADD COMMENTlink modified 15 months ago by mario.zanfardino150 • written 15 months ago by Giuseppe20
Answer: Download TCGA dataset like a S4 object
0
gravatar for mario.zanfardino
15 months ago by
Naples (Italy)
mario.zanfardino150 wrote:

Hi Giuseppe, try curatedTCGA package:

https://bioconductor.org/packages/release/data/experiment/html/curatedTCGAData.html

"This package provides publicly available data from The Cancer Genome Atlas (TCGA) Bioconductor MultiAssayExperiment class objects. These objects integrate multiple assays (e.g. RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. The MultiAssayExperiment class links assay barcodes with patient IDs, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire experiment."

 

ADD COMMENTlink written 15 months ago by mario.zanfardino150
1

Thank you Mario for your answer. I want to download the following dataset :

I executed the following instruction: curatedTCGAData("SKCM","Methylation",F) to download HumanMethylation450 dataset, but the output is not that I want.

I never used this package, can you help me to resolve this problem?

 

ADD REPLYlink written 15 months ago by Giuseppe20
1

This run in my env:

SKCM <- curatedTCGAData(diseaseCode = "SKCM", assays = "Methylation", dry.run = FALSE)

Obviously, the data are in MultiAssayExperiment format (a Bioconductor object-oriented S4 class)(https://bioconductor.org/packages/release/bioc/vignettes/MultiAssayExperiment/inst/doc/MultiAssayExperiment.html).

 

ADD REPLYlink written 15 months ago by mario.zanfardino150
1

Thank you very much for your support! I have last question.. I executed this instruction:

> experiments(SKCM)

ExperimentList class object of length 1:

[1] SKCM_Methylation-20160128: SummarizedExperiment with 485577 rows and 475 columns

I want to convert ExperimentList class to a data frame. How can I do it?

ADD REPLYlink modified 15 months ago • written 15 months ago by Giuseppe20
2

Probably you don't want to convert this to a data frame, but learn to use the SummarizedExperiment class, see for instance here and the package vignette here.

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 24k
1
df <- as.data.frame(wideFormat(SKCM[1:10,1:10 ,"SKCM_Methylation-20160128"], colDataCols = c(1:10)))

df subsetted for 10 Patient, 10 features and 10 colData

ADD REPLYlink written 15 months ago by mario.zanfardino150

thank you so much! The Only problem is that download Methylation dataset is very slow! And the S4 object occupies so much memory

ADD REPLYlink modified 15 months ago • written 15 months ago by Giuseppe20
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