Help batch saving elements of a list into unique files
Okay. Got some lunch, I can think about this with both halves of the brain.
drop_token1<-function(x) {
return(paste(x[2:length(x)],sep="",collapse="."))
}
affnames<-c("X0.Classical.10.11.1_.HuEx.1_0.st.v2..CEL",
"X1.Classical.10.11.1_.HuEx.1_0.st.v2..CEL")
affnames.split<-strsplit(affnames,"[.]")
lapply(affnames.split,drop_token1)
[[1]]
[1] "Classical.10.11.1_.HuEx.1_0.st.v2..CEL"
[[2]]
[1] "Classical.10.11.1_.HuEx.1_0.st.v2..CEL"
This what I get with a toy example. So, I think that:
for(affdf in 1:length(out)) {
names(out[[affdf]])<-lapply(strsplit(names(out[[affdf]]),"[.]),drop_token1)
write.csv(out[[affdf]],file=paste("affymetrix",affdf,".txt",sep=""))
}
should work.
Jim
On Wed, Mar 23, 2016 at 11:16 AM, Christian T Stackhouse (Campus)
<ctstackh at uab.edu> wrote:
I re ran it and this is what I got: 11.1_.HuEx.1_0.st.v2..CEL Should be: 10.11.1_.HuEx.1_0.st.v2..CEL 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 6:24 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
Transcription. I forgot the "collapse" argument when I wrote the email:
drop_token1<-function(x) {
return(paste(x[2:length(x)],sep="",collapse="."))
}
Jim
On Wed, Mar 23, 2016 at 10:14 AM, Christian T Stackhouse (Campus)
<ctstackh at uab.edu> wrote:
Very close! The header now looks like this: c("10", "11", "1_", "HuEx", "1_0", "st", "v2", "", "CEL")
For some reason, it's not concatenating.
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 6:02 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
I think it's the "unlist". I can only test this with one set of made
up names at a time.
names(out[[affdf]])<-
lapply(strsplit(names(out[[affdf]]),"[.]"),drop_token1)
Jim
On Wed, Mar 23, 2016 at 9:57 AM, Christian T Stackhouse (Campus)
<ctstackh at uab.edu> wrote:
This is what I ran:
drop_token1<-function(x) {
+ return(paste(x[2:length(x)],sep="."))
+ }
for(affdf in 1:length(out)) {
+ names(out[[affdf]])<-lapply(unlist(strsplit(names(out[[affdf]]),"[.]")),drop_token1)
+ write.csv(out[[affdf]],file=paste("affymetrix",affdf,".txt",sep=""))
+ }
Error in names(out[[affdf]]) <- lapply(unlist(strsplit(names(out[[affdf]]), :
'names' attribute [1148] must be the same length as the vector [118]
This is what the header was before:
X0.Classical.10.11.1_.HuEx.1_0.st.v2..CEL
There was no output due to the error.
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 5:46 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
Sorry, should be:
names(out[[affdf]])<-
lapply(unlist(strsplit(names(out[[affdf]]),"[.]")),drop_token1)
Jim
On Wed, Mar 23, 2016 at 9:43 AM, Christian T Stackhouse (Campus)
<ctstackh at uab.edu> wrote:
Thank you, Jim. I got this error returned:
Error in strsplit(names(out[[affdf]])) :
argument "split" is missing, with no default
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 5:39 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
Okay, I just snipped off the first token in the header labels assuming
that there would be no more periods. Try this:
drop_token1<-function(x) {
return(paste(x[2:length(x)],sep="."))
}
for(affdf in 1:length(out)) {
names(out[[affdf]])<-lapply(unlist(strsplit(names(out[[affdf]]))),drop_token1)
write.csv(out[[affdf]],file=paste("affymetrix",affdf,".txt",sep=""))
}
Jim
On Wed, Mar 23, 2016 at 9:13 AM, Christian T Stackhouse (Campus)
<ctstackh at uab.edu> wrote:
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
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