Extract Data from RangeSummarizedExperiment
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11 months ago

Hello,

> TCGA_BRCA_LumA
class: RangedSummarizedExperiment 
dim: 56457 567 
metadata(1): data_release
assays(1): HTSeq - FPKM
rownames(56457): ENSG00000000003 ENSG00000000005 ... ENSG00000281912 ENSG00000281920
rowData names(3): ensembl_gene_id external_gene_name original_ensembl_gene_id
colnames(567): TCGA-A2-A1FZ-01A-51R-A14D-07 TCGA-LQ-A4E4-01A-11R-A266-07 ... TCGA-AC-A8OS-01A-12R-A41B-07 TCGA-BH-A0H9-01A-11R-A056-07
colData names(86): barcode patient ... paper_PARADIGM Clusters paper_Pan-Gyn Clusters

I want to extract and save in a csv file the following information from the above RangedSummarizeExperiment object.: FPKM values, ensembl_id and gene_name. Please help me. Thanks a lot.

R TCGA TCGAbiolinks • 338 views
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What have you tried? Try rowdata(TCGA_BRCA_LumA) and assays(TCGA_BRCA_LumA)

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I have tried rowdata which gives me the genomic ranges and assays gives me ensemble ids and FPKM values. How do I combine these?

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Try merge. You may need to get the datasets as data.frame or data.table objects before the merge.

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