Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
JaneShenGunther`TCGADataTool`
buildDesignMatrix  |
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Details and Options
Examples
(9)
Basic Examples
(1)
Given the example data structure for project TCGA-CESC:
In[1]:=
dataStructure=
[{"TCGAProjectData","TCGACESCExceptGenomicDataAllPatients"}];
 | exampleDataTCGA |
In[2]:=
dataStructure//Length
Out[2]=
307
Create the design matrix:
In[3]:=
outcomeProperty="Clinical::Patient::vital_status";predictors={"Clinical::Patient::person_neoplasm_cancer_status","Clinical::Patient::eastern_cancer_oncology_group","Biospecimen::Analyte::analyte_type"};
In[4]:=
designMatrix=
[dataStructure,predictors,outcomeProperty];
| buildDesignMatrix |
In[5]:=
designMatrix//Length
Out[5]=
307
In[6]:=
designMatrix〚;;3〛//Dataset
Out[6]=
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Print statements are generated if properties are discarded from the design matrix:
In[7]:=
predictors={"Clinical::Patient::person_neoplasm_cancer_status","Clinical::Patient::tumor_tissue_site"};
In[8]:=
designMatrix=
[dataStructure,predictors,outcomeProperty];
| buildDesignMatrix |
Wed 15 Feb 2023 12:29:33 1 column(s) dropped because contained only one value: Clinical::Patient::tumor_tissue_site
In[9]:=
designMatrix〚;;3〛//Dataset
Out[9]=
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In[10]:=
dataStructure〚All,"Clinical","Patient",All,"tumor_tissue_site"〛//Union
Out[10]=
{{Cervical}}
Options
(8)
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