Question: Downloding only RNA-Seq Raw counts data from ICGC
0
gravatar for David_emir
9 weeks ago by
David_emir310
India
David_emir310 wrote:

Hi,

I wanted to download RNA-Seq raw counts data from ICGC with samples as columns and gene_symbol as row names. I tried using dplyr but I am not able to get in the proper format. It would be of great help to me if you guys can let me know how to download this.

Sincerely,

Dave

P.S: any package in R would be helpful

raw counts icgc • 173 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by David_emir310

I tried using dplyr but I am not able to get in the proper format.

Share you code here

ADD REPLYlink written 9 weeks ago by bioExplorer3.7k

Thanks Vijay, I tried to cut and paste sample_id rows as a column but it gave me a really messed up results.

ADD REPLYlink written 9 weeks ago by David_emir310

Share you code here

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by ATpoint14k

Hope this will help others, code is here.

mlr --tsv cut -o -f id4,id1,count2 then reshape -s id1,count2 input.tsv

Or

datamash --header-in --whitespace crosstab id4,id1 unique count2 < file

Thanks for your help

ADD REPLYlink modified 9 weeks ago by ATpoint14k • written 9 weeks ago by David_emir310
1
gravatar for David_emir
9 weeks ago by
David_emir310
India
David_emir310 wrote:

Thanks a lot, Guys, I got a solution for this for cross-tabulation (or pivot table) using GNU Datamash and with Miller, using reshape!

Dave

ADD COMMENTlink written 9 weeks ago by David_emir310
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