[R] fetching columns from another file

[William Dunlap]

> -----Original Message-----
> From: Amit [mailto:amitkumartiwary at gmail.com] 
> Sent: Sunday, January 24, 2010 11:23 AM
> To: William Dunlap
> Cc: r-help at r-project.org
> Subject: Re: [R] fetching columns from another file
> 
> I do not want to merge these data frames. But, wish to pick each pair
> of Gene1 & Gene2 from 'ptable' and their corresponding other columns
> from 'table'.

There was a typo in my suggestion.  It should have
had the comma before c("Gene1","Gene2"), not after,
so it selected just those 2 columns.
 PCC <- merge(ptable[,c("Gene1", "Gene2")], table, suffices=c("",""))

It is not clear to me what you want.  If you supply
sample data and desired results that can be copied
and pasted from your mail into an R session someone
should be able to help you.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com 

> 
> On Sun, Jan 24, 2010 at 8:01 PM, William Dunlap 
> <wdunlap at tibco.com> wrote:
> > Have you tried using merge?  E.g., something
> > like
> >   PCC <- merge(ptable[c("Gene1", "Gene2"),], table, 
> suffices=c("",""))
> >
> > By the way, why do you convert the output of
> > read.table to a matrix?  Since you have both
> > character and numeric data columns I think it
> > would make more sense to leave the dataset as
> > a data.frame (which read.table produces).
> >
> > Bill Dunlap
> > Spotfire, TIBCO Software
> > wdunlap tibco.com
> >
> >> -----Original Message-----
> >> From: r-help-bounces at r-project.org
> >> [mailto:r-help-bounces at r-project.org] On Behalf Of Amit
> >> Sent: Sunday, January 24, 2010 10:48 AM
> >> To: r-help at r-project.org
> >> Subject: [R] fetching columns from another file
> >>
> >> Hi! All,
> >>
> >> I am trying to fetch rows from a data frame which matches 
> to first 2
> >> columns of another data frame. Here is the example what I 
> am trying to
> >> do:
> >> > ptable=read.table(file="All.txt",header=T,sep="\t")
> >> > ptable=as.matrix(ptable)
> >> > dim(ptable)
> >> [1] 9275    6
> >> > head(ptable)
> >>      Gene1       Gene2       PCC         PCC3        PCC23
> >>    PCC123
> >> [1,] "3813_f_at" "3884_f_at" "0.9956842" "0.9955455"
> >> "0.9956513" "0.9956171"
> >> [2,] "3884_f_at" "3813_f_at" "0.9956842" "0.9955455"
> >> "0.9956513" "0.9956171"
> >> [3,] "3491_f_at" "3709_f_at" "0.9952116" "0.9951588"
> >> "0.9951601" "0.9950864"
> >> [4,] "3709_f_at" "3491_f_at" "0.9952116" "0.9951588"
> >> "0.9951601" "0.9950864"
> >> [5,] "3371_f_at" "3594_f_at" "0.9946206" "0.9945342"
> >> "0.9946246" "0.9946592"
> >> [6,] "3594_f_at" "3371_f_at" "0.9946206" "0.9945342"
> >> "0.9946246" "0.9946592"
> >> > table=read.table(file="All_GPYeast_m.txt",header=T,sep="\t")
> >> > table=as.matrix(table)
> >> > dim(table)
> >> [1] 9275    6
> >> > head(table)
> >>      Gene1       Gene2       PCC         PCC3        PCC23
> >>    PCC123
> >> [1,] "3491_f_at" "3709_f_at" "0.9953142" "0.9950756"
> >> "0.9954676" "0.9952902"
> >> [2,] "3709_f_at" "3491_f_at" "0.9953142" "0.9950756"
> >> "0.9954676" "0.9952902"
> >> [3,] "3813_f_at" "3884_f_at" "0.9951781" "0.9953901"
> >> "0.9959256" "0.9958152"
> >> [4,] "3884_f_at" "3813_f_at" "0.9951781" "0.9953901"
> >> "0.9959256" "0.9958152"
> >> [5,] "3371_f_at" "3594_f_at" "0.9946130" "0.9938905"
> >> "0.9945572" "0.9945285"
> >> [6,] "3594_f_at" "3371_f_at" "0.9946130" "0.9938905"
> >> "0.9945572" "0.9945285"
> >>
> >> Now, I wish to pick column 1&2 from 'ptable' and their coresponding
> >> columns from 'table' and store it in a variable. I did 
> following and
> >> got error
> >> > PCC=apply(ptable[,c(1,2)],1,function(x)table[x[1],x[2]])
> >> Error in FUN(newX[, i], ...) : subscript out of bounds
> >>
> >> I was expecting something like this
> >> >head(PCC)
> >> [1,] "3813_f_at" "3884_f_at" "0.9951781" "0.9953901"
> >> "0.9959256" "0.9958152"
> >> [2,] "3884_f_at" "3813_f_at" "0.9951781" "0.9953901"
> >> "0.9959256" "0.9958152"
> >> ---------------------
> >> ---------------------
> >>
> >> Please, help!
> >>
> >> regards
> >> Amit
> >>
> >> ______________________________________________
> >> R-help at 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.
> >>
> >
>