I need to transform tab-delimited file like that:
IPR005732 GRMZM2G087165 GRMZM2G146818 GRMZM2G427404
IPR018355 GRMZM2G082642 GRMZM2G310283 GRMZM2G406977 GRMZM5G886785
to list of vectors in
MgsaSets object from
Here's what I have tried.
putative solution 1.
- Read my file to R
- Transform it to list of vectors
I must say that my longest line is 1616 field long, so I moved it to first line of my orginal file to make
read.table read it correctly.
split commands caused termination of
R. I've tried this procedure on much smaller example and it worked ok.
I've tried also to transform my
command looked successful, but produced one entry more than I expected (one gene more), but I don't know how this additional entry looks (I'm not very advanced in S4 objects).
I tried to perform analysis:
xprb is just a list of genes to analysis) and I got this error
Error in mgsa.trampoline(o, sets[!isempty], n, alpha = alpha, beta = beta, :
Set index to high (must not exceed 'n')
putative solution 2.
I tried to read the file to a
MgsaSets object for mgsa package, I tried to create from it appropriate code and paste it to command-line. Problem here is that code like works for small files
but doesn't work for my big file - it is probably too big/long. I got error messages
Error: unexpected ',' in "," after every transition to next line of my pasted code e.g.
Now I really don't have any idea how I can create desired file.