R help - Jul 2010 - a issue about the qutation mark?

Following is a function that I wrote (It is working well). It's a simple
one,
nothing complicated. The only question that I have is a qutation mark issue,
I guess.
#############################################
funcname <- function(trait.file){                                #line1
setwd('/root/subroot')                 # line 2
load('imge.RData')                                        # line3
imge <- imge[,-c(3)]                         # line4
imge <- imge[complete.cases(imge),]   # line5
trait<- read.csv(trait.file)             # line6
ngenes <- nrow(imge)     # line7
nsnp <- nrow(trait)              #line 8
for(i in 1:ngenes) {                             
  for(j in 1:nsnp) {
	if(imge$d1[i]==trait$d1[j] & imge$d2[i]==trait$d2[j]) trait$imgene2[j]
<-
imge$Gene[i]
      else trait$imgene2[j] <- NA
   }
}
   return(trait)
}

hypertension <- funcname("folder/hyper.csv")     # last line
######################################

So, as we all know, when using "read.csv", we need to use qutation
mark out
side the filename which we wanna read in. At first, for line 8, I wrote:
read.csv("trait.file"), at last line, I wrote:
funcname(folder/hyper.csv), but it did not work in this way. Unless I
changed the code to the current one that I showed above, I couldn't get what
I want.  
So, to be straightforward, I will show the difference:
1) the code not working:
read.csv("trait.file")       #line 8
funcname(folder/hyper.csv)  #last line

2) the code working:
read.csv(trait.file)         # line 8
funcname("folder/hyper.csv")   # last line

anyone can tell me why is the difference?

thank you,

karena


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Hi Karena,

On Fri, Jul 16, 2010 at 11:23 AM, karena <dr.jzhou at gmail.com> wrote:
<snip>
> So, as we all know, when using "read.csv", we need to use
qutation mark out
> side the filename which we wanna read in. At first, for line 8, I wrote:
> read.csv("trait.file"), at last line, I wrote:
> funcname(folder/hyper.csv), but it did not work in this way. Unless I
> changed the code to the current one that I showed above, I couldn't get
what
> I want.
> So, to be straightforward, I will show the difference:
> 1) the code not working:
> read.csv("trait.file") ? ? ? #line 8
> funcname(folder/hyper.csv) ?#last line
The problem here is that unquoted commands used to refer to objects
saved in your R working environment (well I may not be using the right
terminology here. But I hope it is clear enough). Also, the /
character is an arithmetic function.  So when you call
funcname(folder/hyper.csv) R will look for an object named folder and
try to divide it by an object named hyper.csv). This could sometimes
make sense, e.g.,

test.fun <- function(x)
{
  (sqrt(x))
}

folder <- 8
hyper.csv <- 2

test.fun(folder/hyper.csv)

but it is not what you want here. In your case, you need to pass a
string to the read.csv function containing the filename.

Even if you got passed this problem, you have another one, which is
that by quoting the argument in read.csv("trait.file") you are asking
read.csv to find a file located in the current working directory named
"trait.file". This is not what you want. You want read.csv to find a
file specified by the argument to the funcname() function.
>
> 2) the code working:
> read.csv(trait.file) ? ? ? ? # line 8
> funcname("folder/hyper.csv") ? # last line
>
> anyone can tell me why is the difference?
This works because you are correctly passing a string to the
read.csv() function. Maybe it helps to try this:

dat <- data.frame(a=rnorm(10), b=rnorm(10))
write.csv(dat, file="test.csv")
file.name <- "test.csv"
dat2 <- read.csv("file.name")
dat2 <- read.csv(file.name)

Best,
Ista
>
> thank you,
>
> karena
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/a-issue-about-the-qutation-mark-tp2291537p2291537.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org

You need to understand the difference between a variable and a value.

In your case that doesn't work, you are supplying a value,
"trait.value".
but you have no file named "trait.value".

In the case that does work you are supplying a variable, trait.value, and
the value contained in that variable is the name of a file that does exist.

It is not quite correct to say that when using read.csv() you put quotation
marks outside the filename. What you do is supply read.csv() with the name
of a file, and that name can either be a character string, or a variable
whose value is a character string.

-Don

On 7/16/10 8:23 AM, "karena" <dr.jzhou at gmail.com> wrote:
> 
> Following is a function that I wrote (It is working well). It's a
simple one,
> nothing complicated. The only question that I have is a qutation mark
issue,
> I guess.
> #############################################
> funcname <- function(trait.file){                                #line1
> setwd('/root/subroot')                 # line 2
> load('imge.RData')                                        # line3
> imge <- imge[,-c(3)]                         # line4
> imge <- imge[complete.cases(imge),]   # line5
> trait<- read.csv(trait.file)             # line6
> ngenes <- nrow(imge)     # line7
> nsnp <- nrow(trait)              #line 8
> for(i in 1:ngenes) {
>   for(j in 1:nsnp) {
> if(imge$d1[i]==trait$d1[j] & imge$d2[i]==trait$d2[j]) trait$imgene2[j]
<-
> imge$Gene[i]
>       else trait$imgene2[j] <- NA
>    }
> }
>    return(trait)
> }
> 
> hypertension <- funcname("folder/hyper.csv")     # last line
> ######################################
> 
> So, as we all know, when using "read.csv", we need to use
qutation mark out
> side the filename which we wanna read in. At first, for line 8, I wrote:
> read.csv("trait.file"), at last line, I wrote:
> funcname(folder/hyper.csv), but it did not work in this way. Unless I
> changed the code to the current one that I showed above, I couldn't get
what
> I want.  
> So, to be straightforward, I will show the difference:
> 1) the code not working:
> read.csv("trait.file")       #line 8
> funcname(folder/hyper.csv)  #last line
> 
> 2) the code working:
> read.csv(trait.file)         # line 8
> funcname("folder/hyper.csv")   # last line
> 
> anyone can tell me why is the difference?
> 
> thank you,
> 
> karena
> 
-- 
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
925 423-1062