How to transform my TCGA data into this?

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4.7 years ago

Dr.Napoleon • 0

I have downloaded TCGA miRNA isoform expression data, and got this data after few steps,i wonder if anyone knows how to transform my data into this ideal form (each SampleID as colnames). thanks a lot!

my data

      SampleId                 miRNA_ID        x
1 TCGA-2K-A9WE-01A-11R-A38N-13 hsa-let-7a-1 7817.009
2 TCGA-2Z-A9J1-01A-11R-A38N-13 hsa-let-7a-1 5915.546
3 TCGA-2Z-A9J2-01A-11R-A38N-13 hsa-let-7a-1 3632.037
4 TCGA-2Z-A9J3-01A-12R-A38N-13 hsa-let-7a-1 6020.645
5 TCGA-2Z-A9J5-01A-21R-A38N-13 hsa-let-7a-1 7183.899
6 TCGA-2Z-A9J6-01A-11R-A38N-13 hsa-let-7a-1 6786.363

ideal form

                   TCGA-2K-A9WE-01A-11R-A38N-13   TCGA-2Z-A9J1-01A-11R-A38N-13                            
1     hsa-let-7a-1    7817.009                      5915.546

R • 1.3k views

ADD COMMENT • link 4.7 years ago by Dr.Napoleon • 0

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This is basic R data handling, I suggest you try out some things as you will need this skill regularily in your career, also to filter out things you are interested in after your analysis.

ADD REPLY • link 4.7 years ago by ATpoint 82k

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Thank for your suggestion! As bioinformatic rookie, these basis problems confused me a lot.

ADD REPLY • link 4.7 years ago by Dr.Napoleon • 0

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You could use tidyverse to do these manipulations, I suggest you to read this: https://r4ds.had.co.nz/introduction.html In the 5th chapter, you will find easy ways to do it. As @ATpoint mentioned, you will need these skills if you are going to work as a bioinformatician/data analyst. Tips : spread/gather functions from tidyverse/tidyr will help you do what you want.