[R] fetching columns from another file

[Amit]

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'.

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
>>
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>