R help - Apr 2012 - Adding more files to list

Hi,

 

I have searched over the last two days to try and sort this problem but
unfortunately I cannot find the correct solution.

I have a main directory  - "Spectra"

In this folder I have two subfolders "Normal"  and "Case"

 

I am using a package MALDIquant for processing of mass spectrometry data, 

The following command will open and list all my files from the Normal
subfolder (70 files containing spectrums)

 

Spectra <- mqReadBrukerFlex(file.path("Spectra/",
"Normal"));

 

How do I add the "Case" folder to the list (another 70 spectra), so
that I
can then process all the files in the same manner and yet maintain their
origin so when I want to do stats analyse on them I can differentiate??

 

Any help would be great, I am very much a beginner,

 

Brian 

 


	[[alternative HTML version deleted]]

Hi Brian,

On Wednesday 25 April 2012 13:15:03 Brian Flatley wrote:
> I have a main directory  - "Spectra"
> 
> In this folder I have two subfolders "Normal"  and
"Case"
The following should be enough:

library("readBrukerFlexData")
Spectra <- mqReadBrukerFlex("Spectra/");
> ...
> The following command will open and list all my files from the Normal
> subfolder (70 files containing spectrums)
>
> Spectra <- mqReadBrukerFlex(file.path("Spectra/",
"Normal"));
> 
> How do I add the "Case" folder to the list (another 70 spectra),
so that I
> can then process all the files in the same manner and yet maintain their
> origin so when I want to do stats analyse on them I can differentiate??
> 
To combine a list you could use "c":

SpectraNormal <- mqReadBrukerFlex(file.path("Spectra/",
"Normal"));
SpectraCase <- mqReadBrukerFlex(file.path("Spectra/",
"Case"));

Spectra <- c(SpectraNormal, SpectraCase);

To maintain the origin you could store the indices:

normal <- 1:length(SpectraNormal);
cases <- (normal+1):(normal+1+length(SpectraCase));

But I would prefer to fetch this information from the MassSpectrum metaData 
slot:

filenames <- sapply(Spectra, function(x) {return(metaData(x)$file); });
normal <- grepl(pattern="/Normal/", x=filenames);
classes <- as.factor(ifelse(normal, "Normal", "Case"));

Now you could access the different cases in the following way:
Spectra[classes=="Normal"]
Spectra[classes=="Case"]

Bye,

Sebastian

As to combining, use c().

as to tracking, keep track of the directory that goes with the file. There are
various ways to do this:

a) keep a vector of filenames, and every time you combine vectors of filenames,
do the same for the vectors of directory names. You will probably need to use
rep() to turn one directory name into a vector of repeated values.

b) an organized way to accomplish option a above is to keep the vectors in data
frames, and use rbind() instead of c() to combine them.

c) you will have to use paste() to combine the paths and filenames before you
open them, so you might want to do so early on and keep track of which category
each falls into using more presentable category names in the auxiliary vector(s)
instead of tracking paths separately.
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Brian Flatley <b.flatley at pgr.reading.ac.uk> wrote:
>Hi,
>
> 
>
>I have searched over the last two days to try and sort this problem but
>unfortunately I cannot find the correct solution.
>
>I have a main directory  - "Spectra"
>
>In this folder I have two subfolders "Normal"  and
"Case"
>
> 
>
>I am using a package MALDIquant for processing of mass spectrometry
>data, 
>
>The following command will open and list all my files from the Normal
>subfolder (70 files containing spectrums)
>
> 
>
>Spectra <- mqReadBrukerFlex(file.path("Spectra/",
"Normal"));
>
> 
>
>How do I add the "Case" folder to the list (another 70 spectra),
so
>that I
>can then process all the files in the same manner and yet maintain
>their
>origin so when I want to do stats analyse on them I can differentiate??
>
> 
>
>Any help would be great, I am very much a beginner,
>
> 
>
>Brian 
>
> 
>
>
>	[[alternative HTML version deleted]]
>
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