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Haznadar, Majda (NIH/NCI) [E]

2015-Jan-07 15:29 UTC

[R] help with looping a specific code

Hi,

I would like to loop a specific code through multiple files ending in .CDF in
the same directory, but I am unsure of how to do that (new to R).

Can someone please help me with this-thank you.

This is the code I would like to loop:
> xr<-xcmsRaw("mh141210xg2_sccs_00101.CDF", profstep=0)
> write.mzdata(xr, file="mh141210xg2_sccs_00101.CDF")
And there are 675 of these .CDF files in the directory that I would like to
apply the code to. Also, when I save the file in the second line of code, I
would like it to have the same name as it previously had, so just re-write the
old file.

Thanks so much for your time!!
Majda

	[[alternative HTML version deleted]]

PIKAL Petr

2015-Jan-07 17:17 UTC

head link

[R] help with looping a specific code

See

?list.files

You can use it to populate object with files in working directory. Then you can
use tis object in loop.

Cheers
Petr
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of
> Haznadar, Majda (NIH/NCI) [E]
> Sent: Wednesday, January 07, 2015 4:30 PM
> To: 'r-help at r-project.org'
> Subject: [R] help with looping a specific code
>
> Hi,
>
> I would like to loop a specific code through multiple files ending in
> .CDF in the same directory, but I am unsure of how to do that (new to
> R).
>
> Can someone please help me with this-thank you.
>
> This is the code I would like to loop:
>
> > xr<-xcmsRaw("mh141210xg2_sccs_00101.CDF", profstep=0)
> > write.mzdata(xr, file="mh141210xg2_sccs_00101.CDF")
>
> And there are 675 of these .CDF files in the directory that I would
> like to apply the code to. Also, when I save the file in the second
> line of code, I would like it to have the same name as it previously
> had, so just re-write the old file.
>
> Thanks so much for your time!!
> Majda
>
>       [[alternative HTML version deleted]]
>
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Franklin Bretschneider

2015-Jan-07 17:21 UTC

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[R] help with looping a specific code

On 2015-01-07 , at 16:29, Haznadar, Majda (NIH/NCI) [E] <majda.haznadar at
nih.gov> wrote:
> Hi,
> 
> I would like to loop a specific code through multiple files ending in .CDF
in the same directory, but I am unsure of how to do that (new to R).
> 
> Can someone please help me with this-thank you.
> 
> This is the code I would like to loop:
> 
>> xr<-xcmsRaw("mh141210xg2_sccs_00101.CDF", profstep=0)
>> write.mzdata(xr, file="mh141210xg2_sccs_00101.CDF")
> 
> And there are 675 of these .CDF files in the directory that I would like to
apply the code to. Also, when I save the file in the second line of code, I
would like it to have the same name as it previously had, so just re-write the
old file.
> 
> Thanks so much for your time!!
> Majda
> 



I use this function to find the appropriate file names, as follows:

getFolder <- function(pat)
	{
	txt=file.choose()
	#cat(txt,'\n')
	pos=0
	fname=basename(txt)
	#cat(paste("\nFilename found is: ",fname,'\n'))
	foln=dirname(txt)
	cat(paste("\nFolder name found is: ",foln,'\n'))
	drtext=dir(foln, pattern=pat, full.names = TRUE)
	#cat('\n\n\n\n') 
	return(drtext)
	}

# it can be called with the appropriate extension as a pattern, e.g. .wav
follist=getFolder("\\.wav")

#  this variable now contains all filenames (complete path names) of the
selected type
# and can be used t read in a loop:

#  for (i in 1:length(follist) {
	#  rad ypur file
	#  do something with it
	#  view or save the results
	#  }

Maybe you can adapt this to your problem.

Success and
Best wishes,



Franklin Bretschneider
Dept of Biology
Utrecht University
bretschr at xs4all.nl

R help - Jan 2015 - help with looping a specific code

[R] help with looping a specific code

[R] help with looping a specific code

[R] help with looping a specific code