Question: DESEQ2 results - write to TSV file
0
gravatar for cpak1981
5 months ago by
cpak1981100
cpak1981100 wrote:

How can I write the values of Formal class 'DESeqResults' [package "DESeq2"] with 6 slots

log2 fold change (MAP): condition treat vs ctrl  
Wald test p-value: condition treat vs ctrl  
DataFrame with 15729 rows and 6 columns  
                   baseMean log2FoldChange      lfcSE      stat       pvalue  
                   <numeric>      <numeric>  <numeric> <numeric>    <numeric>  
A       302.12240     0.35943317 0.15667370  2.294151 2.178181e-02  
B       18.83989     0.20074213 0.29998407  0.669176 5.033832e-01  
C      5946.15326     0.07679007 0.05139921  1.493993 1.351774e-01  
D 6018.48179    -0.09557543 0.07490464 -1.275961 2.019692e-01  
E      7302.76778    -0.31757508 0.05084542 -6.245894 4.213826e-10  

to TSV file? Using readr::write_tsv gives an error

deseq2 • 332 views
ADD COMMENTlink written 5 months ago by cpak1981100
3
gravatar for venu
5 months ago by
venu5.7k
Germany
venu5.7k wrote:

Did you check DEseq 2 manual?

Exporting results to CSV files

ADD COMMENTlink written 5 months ago by venu5.7k

Thanks! - I looked through the manual but not the vignette - the solution is trivial

ADD REPLYlink modified 5 months ago • written 5 months ago by cpak1981100

What do you mean by trivial? Isn't the vignette/manual helpful? Can you post the commands you tried?

ADD REPLYlink written 5 months ago by venu5.7k
2

He's saying it's an easy solution - he just didn't know where to look.

ADD REPLYlink written 5 months ago by jared.andrews071.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 965 users visited in the last hour