[R] Replacing values in dataframes
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$Sample.Id=="10a",Prot.amount["10a",1]) > NAD[1:3,1:3] Sample.Id Main.abs..1 Main.abs..2 10a 15.516 0.04836 0.04994 11a_1109 11a_1109 0.32245 0.36541 11b_1109 11b_1109 0.29293 0.32815 So what I have tried to do is to write a function that would allow me to replace the values automatically of all dataframes. This I just can't get to work. Thank you so much in advance! _ [[elided Hotmail spam]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Replacing values in dataframes
I think this is what you want NAD$Sample.Id <- t(Prot.amount[NAD$Sample.Id]) HTH Schalk Heunis On Sat, Sep 19, 2009 at 12:18 PM, Monna Nygård wrote: > > Hi, > > > > This is a question of a newbie getting into the exciting world of R. > > > > I have several dataframes in the same format as NAD: > > > > > > > NAD[1:3,1:3] > >Sample.Id Main.abs..1 Main.abs..2 > 148 10a 0.04836 0.04994 > 167 11a_1109 0.32245 0.36541 > 173 11b_1109 0.29293 0.32815 > > > What I want to do is to replace the Sample.Id with a corresponding > number.The number i have in another file,called Prot.amount > > > > > Prot.amount[1:3,1] > 10a 11a_1109 11b_1109 > 15.516 38.248 42.297 > > > > > > > row.names(NAD)<-(NAD[,1]) > > NAD$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. > [[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.
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 __ 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.
Re: [R] Replacing values in dataframes
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 28.1849.9272.242
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$Sample.Id <- repla
Re: [R] Replacing values in dataframes
Hi
I believe you are quite near.
r-help-boun...@r-project.org napsal dne 21.09.2009 11:38:29:
>
> Thank you so much for trying to help me.
> Thus, I still can't get it to work.
> I will clearify a bit. If you somehow have time helping me I would much
appreciate it.
> NAD and Prot.amount are both data.frames. There are several different
> dataframes called NAD,NAD1, NAD2 etc. that I would like to run the loop
over.
> Prot.amount has all the samplenames as its row.names and the correct
values as
> Prot.amount[,1]. Thus, the NADs are data.frames with values for the
samples,
> they DO NOT contain all the samples.
> > NAD[1:3,1:3]
> Sample.Id Main.abs..1 Main.abs..2
> 148 10a 0.04836 0.04994
> 167 11a_1109 0.32245 0.36541
> 173 11b_1109 0.29293 0.32815
> > Prot.amount[1:3,1]
> > 10a 11a_1109 11b_1109
> 15.516 38.248 42.297
get rownames to a column named Sample.Id
Prot.amount$Sample.id <- row.names(Prot.amount)
> > 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 28.1849.9272.242
> iddf <- data.frame((Sample.id=row.names(Prot.amount)),
new.id=Prot.amount
> [1:nrow(Prot.amount),])
> Thus,
>
> newNAD <- merge( NAD, iddf)
newNAD <- merge( NAD, Prot.amount, all.x=T)
It shall merge all records from NAD together with values from Prot.amount.
Regards
Petr
>
> > 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 Nygĺrd wrote:
> > >Hi,
> > >
> > >
> > >
> > >This is a questio
