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Gene expression file to Expression matrix

Hi All,

I have an RNAseq gene expression file (Count data) as follows, I need to conduct a Differential gene expression analysis between Patients, for that, I need to have this file as a Matrix of Rows as Genes and columns as counts (samples), how best can I get this as matrix file?

Thanks a lot for your help, Stay safe

Dave

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rna-seq
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updated by Alex Nesmelov Alex Nesmelov • written by David_emir David_emir

You'll need to use something like tidyr::pivot_wider() to get patient_id to columns and retain gene_code as rows. You'll end up picking one of gene_raw/gene_tpm as the values.

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written by Ram Ram

Thanks a lot, RamRS, it's such a great help. Going forward, I have tried your solution and used the following code

bulk_clean<- tidyr::pivot_wider(bulk,id_cols=patient_id,gene_code)

but i m not getting the desired output, please let me know where i am going wrong. thanks again.

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written by David_emir David_emir

What is the output you're getting? Also, please give us the output to: dput(head(bulk, 25)).

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written by Ram Ram

Thanks you RamRS will keep that in mind.

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written by David_emir David_emir

1 answer 

 library(tidyverse)
 your_data %>%
 select(patient_id, gene_code, gene_raw) %>%
 pivot_wider(names_from = patient_id, 
          values_from = gene_raw)

Switch gene_raw to some other expression value if you need.

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written by Alex Nesmelov Alex Nesmelov

Thanks a lot, It worked like a charm

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written by David_emir David_emir

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