Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
JaneShenGunther`TCGADataTool`
importGenomicDataFile  |
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Details and Options
Examples
(3)
Basic Examples
(1)
Download genomic data for a single patient UUID in TCGA-CESC project:
In[1]:=
project="TCGA-CESC";patientUUID={"eb0eb159-732e-43ff-a402-7f2d9f67daa8"};genomicCategory={"Copy Number Variation","Copy Number Segment"};
Evaluate the following cell to download methylation beta values for the selected patient using GDC API:
In[2]:=
EchoTimingdownloadResults=
[project,genomicCategory, "ValidPatientUUIDs"patientUUID,"DownloadTool""GDCAPI"]
 | downloadGenomicData |
Fri 17 Feb 2023 11:52:10 Starting download of 1 files. Total files size
26.057
kB
Fri 17 Feb 2023 11:52:10 Starting download of file Manifest /private/var/folders/9s/ssw_w4pj5tsfxv3r6yrjj1mw0000gn/T/TCGADataTool/FileManifest_TCGA-CESC_CopyNumberVariation_CopyNumberSegment.txt using GDC API.
Fri 17 Feb 2023 11:52:10 Starting download of 1 files.
Fri 17 Feb 2023 11:52:10 Downloading file 60e4bb9f-0fa5-436b-9b18-bdc2483681ae from GDC API to /private/var/folders/9s/ssw_w4pj5tsfxv3r6yrjj1mw0000gn/T/TCGADataTool...
Fri 17 Feb 2023 11:52:11 Download of file 60e4bb9f-0fa5-436b-9b18-bdc2483681ae successfull
⌚
0.964885
Out[2]=
{id60e4bb9f-0fa5-436b-9b18-bdc2483681ae,file_nameCROZE_p_TCGA_254_256_255_N_GenomeWideSNP_6_E07_1301460.grch38.seg.v2.txt,md5sumde289cc7639c7933c5d2c16e4cf6412b,statereleased,file_size26057,case_ids{eb0eb159-732e-43ff-a402-7f2d9f67daa8},num_cases1}
Import the file:
In[3]:=
filePath=FileNameJoin[{$TemporaryDirectory,"TCGADataTool",downloadResults〚1〛["id"],downloadResults〚1〛["file_name"]}]
Out[3]=
/private/var/folders/9s/ssw_w4pj5tsfxv3r6yrjj1mw0000gn/T/TCGADataTool/60e4bb9f-0fa5-436b-9b18-bdc2483681ae/CROZE_p_TCGA_254_256_255_N_GenomeWideSNP_6_E07_1301460.grch38.seg.v2.txt
In[4]:=
fileContent=
[filePath,genomicCategory];
| importGenomicDataFile |
In[5]:=
fileContent//Keys
Out[5]=
{Data,Metadata}
In[6]:=
fileContent["Metadata"]
Out[6]=
{}
In[7]:=
fileContent["Data"]〚;;3〛//Dataset
Out[7]=
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Options
(2)
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""