R help - Oct 2013 - make a file from four individual files. but keys can be missing among files.

Hello,

I have a list of four files. Each file is a list of gene models, and each
gene model has attributes in file columns. The sample_week-over-sample_week
fold change value foreach i in file is in column 5. The gene model ID is in
column 1. To make it more complicated, each gene i may not be found in all
four files. I've written R scripts to try to 1) write a function to iterate
over each file in the working directory, 2) if a gene model, i, is missing
in a file(x), paste an "NA" as the value for that key and 3) make one
master file from the four files with column names as indicated below in the
code.

function(g)(

    for( i in x){
    if( i == NULL)
    print( text("NA"))
        else( print(x[i,5])) #Fold-change value
))

files <- list.files( path=getwd(), pattern="*.txt", full.names=T,
recursive=FALSE)
lapply( files, function(x) {
    x <- read.table( x, header=T) # load file
    # apply function
    out <- function(g)
    # write to file
    write.table( out, "myfile.txt", sep="\t", quote=F,
row.names=F, col.names=T)
    colnames(out)[1] = "ca02"
    colnames(out)[2] = "ca24"
    colnames(out)[3] = "ca48"
    colnames(out)[4] = "ca812"
})
})

The code has no errors, but the file doesn't write to my working directory.
I don't think this path is the problem either.

I've seen the do.call function, thinking this may be the way to go.

Also, if I'd like to add a third column to the master file from the four
files, for example, the BLAST description for that gene model, i, in column
7, how to handle this command as well? I'm kinda new to R but hit a wall
when it comes to this level, as I have had no classroom training on writing
code. Hopefully, I can break on through with your assistance. Thanks much
and have a nice day.
-- 
Franklin

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Hi,

You didn't provide a reproducible example, which makes helping a whole lot
harder.

You're misunderstanding how to define a new function. Not only is g
specified incorrectly, you're creating a new function called out within
your loop and trying to save that to disk.

You need to do more like this

g <- function(args) {
   Does stuff
   Return value
}

And then call it with

out <- g(args)

But it seems to me that merge() might do the trick.

Sarah

On Friday, October 4, 2013, franklin johnson wrote:
> Hello,
>
> I have a list of four files. Each file is a list of gene models, and each
> gene model has attributes in file columns. The sample_week-over-sample_week
> fold change value foreach i in file is in column 5. The gene model ID is in
> column 1. To make it more complicated, each gene i may not be found in all
> four files. I've written R scripts to try to 1) write a function to
iterate
> over each file in the working directory, 2) if a gene model, i, is missing
> in a file(x), paste an "NA" as the value for that key and 3) make
one
> master file from the four files with column names as indicated below in the
> code.
>
> function(g)(
>
>     for( i in x){
>     if( i == NULL)
>     print( text("NA"))
>         else( print(x[i,5])) #Fold-change value
> ))
>
> files <- list.files( path=getwd(), pattern="*.txt",
full.names=T,
> recursive=FALSE)
> lapply( files, function(x) {
>     x <- read.table( x, header=T) # load file
>     # apply function
>     out <- function(g)
>     # write to file
>     write.table( out, "myfile.txt", sep="\t", quote=F,
row.names=F,
> col.names=T)
>     colnames(out)[1] = "ca02"
>     colnames(out)[2] = "ca24"
>     colnames(out)[3] = "ca48"
>     colnames(out)[4] = "ca812"
> })
> })
>
> The code has no errors, but the file doesn't write to my working
directory.
> I don't think this path is the problem either.
>
> I've seen the do.call function, thinking this may be the way to go.
>
> Also, if I'd like to add a third column to the master file from the
four
> files, for example, the BLAST description for that gene model, i, in column
> 7, how to handle this command as well? I'm kinda new to R but hit a
wall
> when it comes to this level, as I have had no classroom training on writing
> code. Hopefully, I can break on through with your assistance. Thanks much
> and have a nice day.
> --
> Franklin
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org <javascript:;> 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.
>

-- 
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org

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