Hi John and Bert,
Thank you so much for your replies. Both of your scripts worked well, so
now I've learnt two ways to do it. :)
Bert: I was not very clear on what I wanted to do. I just would like to
calculate the residues shown in the table, not all residues. The
*apply*functions
* *are amazing!
John: as I am still digesting the codes, I am not sure if I fully
understood the argument .(variables, value) in the *ddply* line. The
description of *ddply* says that .variables show the variables to split
data frame by, as quoted variables, a formula or character vector. So does
.(variables, value) tell R to split the data frame by values, which are the
types of amino acid residues?
Thank you all again.
Cheers,
Zhao
2012/7/24 Bert Gunter <gunter.ber...@gene.com>
> ... and I neglected to mention that f = myfiles[,2]
>
> Sigh.... More coffee needed.
>
> -- Bert
>
> On Tue, Jul 24, 2012 at 9:43 AM, Bert Gunter <bgun...@gene.com> wrote:
> > Sorry. Typo in my previous. Should be:
> >
> >> sapply(myfile[,-c(1,2)],function(x)prop.table(tapply(f,x,sum)))
> > $X1
> > L R T
> > 0.91491320 0.03675651 0.04833030
> >
> > $X2
> > E M
> > 0.9827278 0.0172722
> >
> > $X3
> > N Y
> > 0.0483303 0.9516697
> >
> > $X4
> > I L Q
> > 0.8976410 0.0850868 0.0172722
> >
> > $X5
> > I V
> > 0.9516697 0.0483303
> >
> > $X6
> > P S
> > 0.96324349 0.03675651
> >
> > $X7
> > D E G
> > 0.8976410 0.0540287 0.0483303
> >
> > $X8
> > A C
> > 0.9827278 0.0172722
> >
> >
> >
> > On Tue, Jul 24, 2012 at 9:37 AM, Bert Gunter <bgun...@gene.com> wrote:
> >> OK, I admit it: I re-read what you wrote and now I'm confused. Is:
> >>
> >>> sapply(myfile[,-c(1,2)],function(x)prop.table(tapply(f,x)))
> >>
> >> X1 X2 X3 X4 X5 X6 X7 X8
> >> [1,] 0.1428571 0.2 0.2857143 0.125 0.2 0.2 0.125 0.2
> >> [2,] 0.4285714 0.2 0.1428571 0.250 0.4 0.2 0.375 0.2
> >> [3,] 0.1428571 0.4 0.2857143 0.375 0.2 0.2 0.250 0.4
> >> [4,] 0.2857143 0.2 0.2857143 0.250 0.2 0.4 0.250 0.2
> >>
> >> what you want?
> >>
> >> -- Bert
> >> On Tue, Jul 24, 2012 at 9:17 AM, Bert Gunter <bgun...@gene.com> wrote:
> >>> The OP's request is a bit ambiguous to me: at a given residue, do you
> >>> wish to calculate the proportions for only those amino acids that
> >>> appear at that residue, or do you wish to include the proportions for
> >>> all amino acids, some of which might then be 0.
> >>>
> >>> Assuming the former, then I don't think one needs to go to the lengths
> >>> described by John below.
> >>>
> >>> Using your example (thanks!), the following seems to suffice:
> >>>
> >>>> sapply(myfile[,-c(1,2)],function(x)prop.table(table(x)))
> >>>
> >>> $X1
> >>> x
> >>> L R T
> >>> 0.50 0.25 0.25
> >>>
> >>> $X2
> >>> x
> >>> E M
> >>> 0.75 0.25
> >>>
> >>> $X3
> >>> x
> >>> N Y
> >>> 0.25 0.75
> >>>
> >>> $X4
> >>> x
> >>> I L Q
> >>> 0.25 0.50 0.25
> >>>
> >>> $X5
> >>> x
> >>> I V
> >>> 0.75 0.25
> >>>
> >>> $X6
> >>> x
> >>> P S
> >>> 0.75 0.25
> >>>
> >>> $X7
> >>> x
> >>> D E G
> >>> 0.25 0.50 0.25
> >>>
> >>> $X8
> >>> x
> >>> A C
> >>> 0.75 0.25
> >>>
> >>>
> >>> This could, of course, then be modified to add zero proportions for
> >>> all non-appearing amino acids.
> >>>
> >>> -- Cheers,
> >>> Bert
> >>>
> >>> On Tue, Jul 24, 2012 at 8:18 AM, John Kane <jrkrid...@inbox.com>
> wrote:
> >>>>
> >>>> I think this does what you want using two packages, plyr and
> reshape2 that
> >>>> you may have to install. If so install.packages("plyr",
> "reshape2") should
> >>>> do the trick.
> >>>> library(plyr)
> >>>> library(reshape2)
> >>>> # using supplied file 'myfile" from below
> >>>> time0total = sum(myfile[,2])
> >>>> mydata <- myfile[, 2:10]
> >>>> md1 <- melt(mydata, id = "Time_zero")
> >>>> ddply(md1, .(variable, value), summarise, sum =
> sum(Time_zero)/time0total)
> >>>>
> >>>>
> >>>> John Kane
> >>>> Kingston ON Canada
> >>>>
> >>>> -----Original Message-----
> >>>> From: z...@cornell.edu
> >>>> Sent: Tue, 24 Jul 2012 10:25:21 -0400
> >>>> To: jrkrid...@inbox.com
> >>>> Subject: Re: [R] How to do the same thing for all levels of a
> column?
> >>>>
> >>>> Hi John,
> >>>> Thank you for the tips. My apologies about the unreadable sample
> data...
> >>>> So here is the output of the sample data, and hopefully it works
> this time
> >>>> :)
> >>>> myfile <- structure(list(Proteins = structure(1:4, .Label =
> c("p1", "p2",
> >>>> "p3", "p4"), class = "factor"), Time_zero = c(0.0050723, 0.0002731,
> >>>> 9.76e-05, 0.0002077), X1 = structure(c(1L, 3L, 1L, 2L), .Label =
> c("L",
> >>>> "R", "T"), class = "factor"), X2 = structure(c(1L, 1L, 2L, 1L
> >>>> ), .Label = c("E", "M"), class = "factor"), X3 = structure(c(2L,
> >>>> 1L, 2L, 2L), .Label = c("N", "Y"), class = "factor"), X4 =
> structure(c(1L,
> >>>> 2L, 3L, 2L), .Label = c("I", "L", "Q"), class = "factor"),
> X5 =
> >>>> structure(c(1L,
> >>>> 2L, 1L, 1L), .Label = c("I", "V"), class = "factor"), X6 =
> structure(c(1L,
> >>>> 1L, 1L, 2L), .Label = c("P", "S"), class = "factor"), X7 =
> structure(c(1L,
> >>>> 3L, 2L, 2L), .Label = c("D", "E", "G"), class = "factor"),
> X8 =
> >>>> structure(c(1L,
> >>>> 1L, 2L, 1L), .Label = c("A", "C"), class = "factor")),
> .Names =
> >>>> c("Proteins",
> >>>> "Time_zero", "X1", "X2", "X3", "X4", "X5", "X6", "X7", "X8"),
> row.names =
> >>>> c(NA,
> >>>> 4L), class = "data.frame")
> >>>> And here is my original question:
> >>>> 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.
> >>>>
> >>>> 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?
> >>>>
> >>>> Thanks a lot!
> >>>>
> >>>> Regards,
> >>>>
> >>>> Zhao
> >>>> 2012/7/24 John Kane <[1]jrkrid...@inbox.com>
> >>>>
> >>>> 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: [2]z...@cornell.edu
> >>>> > Sent: Mon, 23 Jul 2012 18:01:11 -0400
> >>>> > To: [3]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]]
> >>>> >
> >>>> > ______________________________________________
> >>>> > [4]R-help@r-project.org mailing list
> >>>> > [5]https://stat.ethz.ch/mailman/listinfo/r-help
> >>>> > PLEASE do read the posting guide
> >>>> > [6]http://www.R-project.org/posting-guide.html
> >>>> > and provide commented, minimal, self-contained, reproducible
> code.
> >>>> ____________________________________________________________
> >>>> FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks &
> orcas on
> >>>> your desktop!
> >>>> Check it out at [7]http://www.inbox.com/marineaquarium
> >>>>
> >>>> --
> >>>> Zhao JIN
> >>>> Ph.D. Candidate
> >>>> Ruth Ley Lab
> >>>> 467 Biotech
> >>>> Field of Microbiology, Cornell University
> >>>> Lab: 607.255.4954
> >>>> Cell: 412.889.3675
> >>>> _________________________________________________________________
> >>>>
> >>>> [8]3D Earth Screensaver Preview
> >>>> Free 3D Earth Screensaver
> >>>> Watch the Earth right on your desktop! Check it out
> at
> >>>> [9]www.inbox.com/earth
> >>>>
> >>>> References
> >>>>
> >>>> 1. mailto:jrkrid...@inbox.com
> >>>> 2. mailto:z...@cornell.edu
> >>>> 3. mailto:r-help@r-project.org
> >>>> 4. mailto:R-help@r-project.org
> >>>> 5. https://stat.ethz.ch/mailman/listinfo/r-help
> >>>> 6. http://www.R-project.org/posting-guide.html
> >>>> 7. http://www.inbox.com/marineaquarium
> >>>> 8. http://www.inbox.com/earth
> >>>> 9. http://www.inbox.com/earth
> >>>> ______________________________________________
> >>>> R-help@r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>>> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> >>>> and provide commented, minimal, self-contained, reproducible code.
> >>>
> >>>
> >>>
> >>> --
> >>>
> >>> Bert Gunter
> >>> Genentech Nonclinical Biostatistics
> >>>
> >>> Internal Contact Info:
> >>> Phone: 467-7374
> >>> Website:
> >>>
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
> >>
> >>
> >>
> >> --
> >>
> >> Bert Gunter
> >> Genentech Nonclinical Biostatistics
> >>
> >> Internal Contact Info:
> >> Phone: 467-7374
> >> Website:
> >>
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
> >
> >
> >
> > --
> >
> > Bert Gunter
> > Genentech Nonclinical Biostatistics
> >
> > Internal Contact Info:
> > Phone: 467-7374
> > Website:
> >
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
>
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
>
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
--
Zhao JIN
Ph.D. Candidate
Ruth Ley Lab
467 Biotech
Field of Microbiology, Cornell University
Lab: 607.255.4954
Cell: 412.889.3675
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