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
[[alternative HTML version deleted]]
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