thr3ads.net - R help - [R] Help batch saving elements of a list into unique files [Mar 2016]

If this information is useful, please help other people find it:
Share via:

Christian T Stackhouse (Campus)

2016-Mar-22 19:32 UTC

[R] Help batch saving elements of a list into unique files

Hello!


The overall goal I have is taking a large data frame and splitting it into
several smaller data frames (preserving column headers) which I can save as txt
files to feed into my APACHE ANY23 server for conversion into RDF.


This is what I call to split up the original file:


out <- split(affymetrix, (seq(nrow(affymetrix))-1) %/% 140)


I have a list (out) of length 187 for which each element is a dataframe. I want
to iteratively save each data frame as a separate tab file with a naming
structure such as: affymetrix1.txt, affymetrix2.txt, ... affymetrix187.txt


Before that, I need to modify the headers to remove a prefix "X0. , X1.,
... X187." that was introduced during my original splitting. I need to
remove all characters before and including the first "."


If anyone has a better way of doing this, please let me know. Otherwise, help
with how to perform batch editing of the headers and batch saving of the files
would be greatly appreciated!


Best,

Christian T. Stackhouse | Graduate Student
GBS Neuroscience Theme
Department of Neurosurgery
Department of Radiation Oncology
UAB | The University of Alabama at Birmingham
Hazelrig-Salter Radiation Oncology Center | 1700 6th Ave S | Birmingham, AL
35233
M: 919.724.6890 | ctstackh at uab.edu | cstackhouse at uabmc.edu | ctstackh at
gmail.com

uab.edu<http://uab.edu/>
Knowledge that will change your world


	[[alternative HTML version deleted]]

Jim Lemon

2016-Mar-22 21:48 UTC

head link

[R] Help batch saving elements of a list into unique files

Hi Christian,
This untested script might get you going (assuming you want a CSV format):

for(affdf in 1:length(out)) {
 names(out[[affdf]])<-lapply(strsplit(names(out[[affdf]]),"[.]"),"[",2)
 write.csv(out[[affdf]],file=paste("affymetrix",affdf,".txt",sep=""))
}

Jim


On Wed, Mar 23, 2016 at 6:32 AM, Christian T Stackhouse (Campus)
<ctstackh at uab.edu> wrote:> Hello!
>
>
> The overall goal I have is taking a large data frame and splitting it into
several smaller data frames (preserving column headers) which I can save as txt
files to feed into my APACHE ANY23 server for conversion into RDF.
>
>
> This is what I call to split up the original file:
>
>
> out <- split(affymetrix, (seq(nrow(affymetrix))-1) %/% 140)
>
>
> I have a list (out) of length 187 for which each element is a dataframe. I
want to iteratively save each data frame as a separate tab file with a naming
structure such as: affymetrix1.txt, affymetrix2.txt, ... affymetrix187.txt
>
>
> Before that, I need to modify the headers to remove a prefix "X0. ,
X1., ... X187." that was introduced during my original splitting. I need to
remove all characters before and including the first "."
>
>
> If anyone has a better way of doing this, please let me know. Otherwise,
help with how to perform batch editing of the headers and batch saving of the
files would be greatly appreciated!
>
>
> Best,
>
> Christian T. Stackhouse | Graduate Student
> GBS Neuroscience Theme
> Department of Neurosurgery
> Department of Radiation Oncology
> UAB | The University of Alabama at Birmingham
> Hazelrig-Salter Radiation Oncology Center | 1700 6th Ave S | Birmingham, AL
35233
> M: 919.724.6890 | ctstackh at uab.edu | cstackhouse at uabmc.edu | ctstackh
at gmail.com
>
> uab.edu<http://uab.edu/>
> Knowledge that will change your world
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.

Christian T Stackhouse (Campus)

2016-Mar-22 22:13 UTC

head link

[R] Help batch saving elements of a list into unique files

Jim,

It worked! It wrote out the files, but unfortunately, it didn't work for the
file headers. I should have mentioned this is what the headers look like:
X0.Classical.10.11.1_.HuEx.1_0.st.v2..CEL
After running your script, that header changes to: 10. I'd just like to
remove the "X0." prefix or in the case of file 189 the
"X188." prefix leaving: Classical.10.11.1_.HuEx.1_0.st.v2..CEL

Thank you so much for your help! I'll try playing with it myself, but if you
have any further insights they would be greatly appreciated!

Best,

Christian T. Stackhouse | Graduate Student
GBS Neuroscience Theme
Department of Neurosurgery
Department of Radiation Oncology
UAB | The University of Alabama at Birmingham
Hazelrig-Salter Radiation Oncology Center | 1700 6th Ave S | Birmingham, AL
35233
M: 919.724.6890 | ctstackh at uab.edu | cstackhouse at uabmc.edu | ctstackh at
gmail.com

uab.edu
Knowledge that will change your world


________________________________________
From: Jim Lemon <drjimlemon at gmail.com>
Sent: Tuesday, March 22, 2016 4:48 PM
To: Christian T Stackhouse (Campus)
Cc: r-help at r-project.org
Subject: Re: [R] Help batch saving elements of a list into unique files

Hi Christian,
This untested script might get you going (assuming you want a CSV format):

for(affdf in 1:length(out)) {
 names(out[[affdf]])<-lapply(strsplit(names(out[[affdf]]),"[.]"),"[",2)
 write.csv(out[[affdf]],file=paste("affymetrix",affdf,".txt",sep=""))
}

Jim


On Wed, Mar 23, 2016 at 6:32 AM, Christian T Stackhouse (Campus)
<ctstackh at uab.edu> wrote:> Hello!
>
>
> The overall goal I have is taking a large data frame and splitting it into
several smaller data frames (preserving column headers) which I can save as txt
files to feed into my APACHE ANY23 server for conversion into RDF.
>
>
> This is what I call to split up the original file:
>
>
> out <- split(affymetrix, (seq(nrow(affymetrix))-1) %/% 140)
>
>
> I have a list (out) of length 187 for which each element is a dataframe. I
want to iteratively save each data frame as a separate tab file with a naming
structure such as: affymetrix1.txt, affymetrix2.txt, ... affymetrix187.txt
>
>
> Before that, I need to modify the headers to remove a prefix "X0. ,
X1., ... X187." that was introduced during my original splitting. I need to
remove all characters before and including the first "."
>
>
> If anyone has a better way of doing this, please let me know. Otherwise,
help with how to perform batch editing of the headers and batch saving of the
files would be greatly appreciated!
>
>
> Best,
>
> Christian T. Stackhouse | Graduate Student
> GBS Neuroscience Theme
> Department of Neurosurgery
> Department of Radiation Oncology
> UAB | The University of Alabama at Birmingham
> Hazelrig-Salter Radiation Oncology Center | 1700 6th Ave S | Birmingham, AL
35233
> M: 919.724.6890 | ctstackh at uab.edu | cstackhouse at uabmc.edu | ctstackh
at gmail.com
>
> uab.edu<http://uab.edu/>
> Knowledge that will change your world
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.

R help - Mar 2016 - Help batch saving elements of a list into unique files

[R] Help batch saving elements of a list into unique files

[R] Help batch saving elements of a list into unique files

[R] Help batch saving elements of a list into unique files