First thing is to supply the data in a useable format. As is it is
essenatially unreadable. All R-beginners do this. :)
Have a look at the dput function (?dput) for a good way to supply sample data
in an email.
If you have a large dataset probably a few dozen lines of data would be fine.
Something like dput(head(mydata)) should be fine. Just copy and paste the
output into your email.
Welcome to R. I think you will like it.
John Kane
Kingston ON Canada
> -----Original Message-----
> From: z...@cornell.edu
> Sent: Mon, 23 Jul 2012 18:01:11 -0400
> To: r-help@r-project.org
> Subject: [R] How to do the same thing for all levels of a column?
>
> Dear all,
>
>
>
> I am a R beginner, and I am looking for a way to do the same thing for
> all
> levels of a column in a table.
>
>
>
> Basically, I have a bunch of protein sequences composed of different
> amino
> acid residues, and each residue is represented by an uppercase letter. I
> want to calculate the ratio of different amino acid residues at each
> position of the proteins. Here is an example table:
>
> Proteins
>
> Time_zero
>
> 1
>
> 2
>
> 3
>
> 4
>
> 5
>
> 6
>
> 7
>
> 8
>
> p1
>
> 0.0050723
>
> L
>
> E
>
> Y
>
> I
>
> I
>
> P
>
> D
>
> A
>
> p2
>
> 0.0002731
>
> T
>
> E
>
> N
>
> L
>
> V
>
> P
>
> G
>
> A
>
> p3
>
> 9.757E-05
>
> L
>
> M
>
> Y
>
> Q
>
> I
>
> P
>
> E
>
> C
>
> p4
>
> 0.0002077
>
> R
>
> E
>
> Y
>
> L
>
> I
>
> S
>
> E
>
> A
>
>
>
> If I name this table as myfile.txt, I have the following scripts to
> calculate the ratio of each amino acid residue at position 1:
>
> # showing levels of the 3rd column, which means the types of residues
>
> >myfile[,3]
>
>
>
> # calculating the ratio of L
>
> >list=c(which(myfile[,3]=="L"))
>
> >time0total=sum(myfile[,2])
>
> >AA_L=0
>
> >for (i in 1:length(list)){AA_L=sum(myfile[list[[i]],2]+AA_L)}
>
> >ratio_L=AA_L/time0total
>
>
>
> So how can I write a script to do the same thing for the other two levels
> (T and R) in column 3, and also do this for every column that contains
> amino acid residues?
>
>
>
> Many thanks for any help you could give me on this topic! :)
>
>
>
> Regards,
>
> Zhao
> --
> Zhao JIN
> Ph.D. Candidate
> Ruth Ley Lab
> 467 Biotech
> Field of Microbiology, Cornell University
> Lab: 607.255.4954
> Cell: 412.889.3675
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
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