fetching columns from another file

-----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'.

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