Meaning of subtype_methylation.Clusters , subtype_miRNA.Clusters, subtype_CN.Clusters
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vera • 0
@vera-12278
Last seen 7.1 years ago

Hi all,

I have just started exploring the possibilities of TCGAbiolinks and have a question about the numbers given for the sample features "subtype_methylation.Clusters" , "subtype_miRNA.Clusters" and "subtype_CN.Clusters".

These are retrieved together with other clinical and subtype information on the samples by accessing the colData of the prepared gene expression data using TCGAbiolinks and SummarizedExperiment. The subtype_methylation.Clusters etc. give a number to each sample (e.g 1-6), but I don't know where these numbers stand for.. I am not working with the miRNA/methylation/CN data, but it would be nice to show that the expression of my genes of interests correlates to certain profiles of CN aberrations etc., and this may be an easy way to do so. 

Does anyone know if these numbers correspond to some predefined set of methylation/miRNA/CN gene clusters, to which the samples were elsewhere classified based on their methylation/miRNA/CN data, and if the corresponding genes can be retrieved somewhere? 

 

some extra info:

query<-GDCquery(project="TCGA-BRCA", 
                                   legacy=TRUE,
                                   data.category="Gene expression", 
                                   data.type="Gene expression quantification", 
                                   platform="Illumina HiSeq",
                                   file.type="normalized_results", 
                                   experimental.strategy="RNA-seq" ,
                                   sample.type="Primary solid Tumor")
GDCdownload(query)
data<-GDCprepare(query)
sample.information<-colData(data)

>> the columns "subtype_methylation.Clusters" , "subtype_miRNA.Clusters" and "subtype_CN.Clusters" are given within this sample.information dataframe

 

tcgabiolinks • 764 views
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Entering edit mode
@tiago-chedraoui-silva-8877
Last seen 3.6 years ago
Brazil - University of São Paulo/ Los A…
Hi, Every Field with the prefix subtype came from a marker TCGA paper. You can find the list of papers on the vignette. The meaning of each column should be described in the article. Best regards, Tiago Em 2 de fev de 2017 4:45 PM, "vera [bioc]" <noreply@bioconductor.org> escreveu: > Activity on a post you are following on support.bioconductor.org > > User vera <https: support.bioconductor.org="" u="" 12278=""/> wrote Question: > Meaning of subtype_methylation.Clusters , subtype_miRNA.Clusters, > subtype_CN.Clusters <https: support.bioconductor.org="" p="" 91963=""/>: > > Hi all, > > I have just started exploring the possibilities of TCGAbiolinks and have a > question about the numbers given for the sample features > "subtype_methylation.Clusters" , "subtype_miRNA.Clusters" and > "subtype_CN.Clusters". > > These are retrieved together with other clinical and subtype information > on the samples by accessing the colData of the prepared gene expression > data using TCGAbiolinks and SummarizedExperiment. The > subtype_methylation.Clusters etc. give a number to each sample (e.g 1-6), > but I don't know where these numbers stand for.. I am not working with the > miRNA/methylation/CN data, but it would be nice to show that the expression > of my genes of interests correlates to certain profiles of CN aberrations > etc., and this may be an easy way to do so. > > Does anyone know if these numbers correspond to some predefined set of > methylation/miRNA/CN gene clusters, to which the samples were elsewhere > classified based on their methylation/miRNA/CN data, and if the > corresponding genes can be retrieved somewhere? > > > > some extra info: > > query<-GDCquery(project="TCGA-BRCA") > GDCdownload(query) > data<-GDCprepare(query) > sample.information<-colData(data) > > >> the columns "subtype_methylation.Clusters" , "subtype_miRNA.Clusters" > and "subtype_CN.Clusters" are given within this sample.information dataframe > > > ------------------------------ > > Post tags: tcgabiolinks > > You may reply via email or visit Meaning of subtype_methylation.Clusters , subtype_miRNA.Clusters, subtype_CN.Clusters >
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