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

[Jim Lemon]

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
>>>>>
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
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