Thank you so much for trying to help me.
Thus, I still can't get it to work.
I will clearify a bit. If you somehow have time helping me I would much
appreciate it.
NAD and Prot.amount are both data.frames. There are several different
dataframes called NAD,NAD1, NAD2 etc. that I would like to run the loop over.
Prot.amount has all the samplenames as its row.names and the correct values as
Prot.amount[,1]. Thus, the NADs are data.frames with values for the samples,
they DO NOT contain all the samples.
> NAD[1:3,1:3]
Sample.Id Main.abs..1 Main.abs..2
148 10a 0.04836 0.04994
167 11a_1109 0.32245 0.36541
173 11b_1109 0.29293 0.32815
> Prot.amount[1:3,1]
> 10a 11a_1109 11b_1109
15.516 38.248 42.297
> dim(Prot.amount)
[1] 30 1
> dim(NAD)
[1] 23 12
The thing I want to do is to replace the sample name with the correct
Prot.amount. So that in all dataframes where I have for instance sample 10a i
want to have a column with its corresponding prot.amount, here 15.516.
Sample.id=row.names(Prot.amount)
gives a vector with all the correct sample.id's
new.id=Prot.amount[1:nrow(Prot.amount),] gives all the samples and their
correct prot.amounts.
> new.id[1:8]
10a 11a_1109 11b_1109 12a_1109 12b_1109 1a_1109 2a 2a_1009
15.516 38.248 42.297 36.134 25.467 28.184 9.927 2.242
iddf <- data.frame((Sample.id=row.names(Prot.amount)),
new.id=Prot.amount[1:nrow(Prot.amount),])
Thus,
newNAD <- merge( NAD, iddf)
> newNAD[4,]
Sample.Id Main.abs..1 Main.abs..2 Main.abs..3 Main.abs..4 Main.abs..5
Main.abs..6 Main.abs..7 Main.abs..8 Main.abs..9
4 12a_1109 0.26291 0.26794 0.27809 0.28948 0.29654
0.3051 0.31388 0.3223 0.33066
Main.abs..10 Main.abs..11 X.Sample.id...row.names.Prot.amount.. new.id
4 0.33806 0.34577 10a 15.516
Produces the correct looking dataframe, only that the first sample.id and
corresponding Prot.amount gets merged to all rows.
So what I need to do is a loop. This is my suggestion:
Changing<-function(A){
tmp<-mat.or.vec(nr=nrow(A),nc=1)
newNAD <-mat.or.vec(nr=nrow(A),nc=1)
for (j in 1:nrow(A)) {
tmp[j] <- data.frame((A$Sample.id=row.names(Prot.amount)),
(A$new.id=Prot.amount[j,]))
newNAD <- merge(A[j,], tmp[j])
}
newNAD
}
Thus, of course it doesn't work that easily. This is becouse
> Changing(NAD)
Error in `$<-.data.frame`(`*tmp*`, "Sample.id", value = c("10a", "11a_1109", :
replacement has 30 rows, data has 23
meaning the dataframe NAD with the samples have 23 samples, the Prot.amounts
file have 30 different samples and their corresponding values. How do I include
into the loop that I only want to replace those Prot.amount values found in the
NAD dataframe?
Thank you so much!
> Date: Sat, 19 Sep 2009 21:35:31 -0700
> To: monn...@hotmail.com; r-help@r-project.org
> From: m...@llnl.gov
> Subject: Re: [R] Replacing values in dataframes
>
> What I would probably do is along these lines:
>
> iddf <- data.frame(Sample.id=names(Prot.amount), new.id=Prot.amount[1,])
>
> newNAD <- merge( NAD, iddf)
>
> This is not tested, but it looks right to me,
> assuming I understand the structure of what
> you're trying to do.
>
> I'm also assuming that NAD has more than three
> rows, and that Prot.amount has as many columns as
> NAD has rows. And that you just showed us the
> first three rows of NAD and first three columns
> of Prot.amount in order to keep the email simple.
>
> One final note ... if Prot.amount is an object
> within R, it is *not* a file. You may have read
> it in from a file, of course, but it isn't a file
> inside R. I'm assuming it's a dataframe.
>
> -Don
>
> At 1:18 PM +0300 9/19/09, Monna Nygård wrote:
> >Hi,
> >
> >
> >
> >This is a question of a newbie getting into the exciting world of R.
> >
> >
> >
> >I have several dataframes in the same format as NAD:
> >
> >
> >
> >
> >
> >> NAD[1:3,1:3]
> >
> > Sample.Id Main.abs..1 Main.abs..2
> >148 10a 0.04836 0.04994
> >167 11a_1109 0.32245 0.36541
> >173 11b_1109 0.29293 0.32815
> >
> >
> >What I want to do is to replace the Sample.Id
> >with a corresponding number.The number i have in
> >another file,called Prot.amount
> >
> >
> >
> >> Prot.amount[1:3,1]
> > 10a 11a_1109 11b_1109
> > 15.516 38.248 42.297
> >
> >
> >
> >
> >
> >> row.names(NAD)<-(NAD[,1])
> >> NAD$Sample.Id <- replace(NAD$Sample.Id,
> >>NAD$Sample.Id=="10a",Prot.amount["10a",1])
> >
> >> NAD[1:3,1:3]
> > Sample.Id Main.abs..1 Main.abs..2
> >10a 15.516 0.04836 0.04994
> >11a_1109 11a_1109 0.32245 0.36541
> >11b_1109 11b_1109 0.29293 0.32815
> >
> >
> >
> >So what I have tried to do is to write a
> >function that would allow me to replace the
> >values automatically of all dataframes. This I
> >just can't get to work.
> >
> >
> >
> >Thank you so much in advance!
> >
> >_________________________________________________________________
> >[[elided Hotmail spam]]
> >
> > [[alternative HTML version deleted]]
> >
> >______________________________________________
> >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.
>
>
> --
> ---------------------------------
> Don MacQueen
> Lawrence Livermore National Laboratory
> Livermore, CA, USA
> 925-423-1062
> m...@llnl.gov
> ---------------------------------
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