On Thu, Jun 27, 2019 at 10:48 AM Spencer Brackett <
spbracket...@saintjosephhs.com> wrote:
> Hello,
>
> Was that helpful in clarifying?
>
> Best,
>
> Spencer
>
> On Tue, Jun 25, 2019 at 5:14 PM Spencer Brackett <
> spbracket...@saintjosephhs.com> wrote:
>
>> Thank you! The following is the result of the corrected code using
>> >cnames ....
>>
>> > cnames
>> [1] "sample.NA.NA.NANA" "TCGA.27.1832.01.NA.NA.NANA"
>> "TCGA.27.1831.01.NA.NA.NANA"
>> [4] "TCGA.28.5216.01.NA.NA.NANA" "TCGA.16.0846.01.NA.NA.NANA"
>> "TCGA.28.5218.01.NA.NA.NANA"
>> [7] "TCGA.06.0178.01.NA.NA.NANA" "TCGA.06.0238.01.NA.NA.NANA"
>> "TCGA.06.0125.01.NA.NA.NANA"
>> [10] "TCGA.06.0219.01.NA.NA.NANA"
>>
>> And then the first 2 lines of the output for the corrected paste() bit of
>> the original coding...
>>
>> [[1]]
>> [1] "sample.NA.NA.NA"
>>
>> [[2]]
>> [1] "TCGA.27.1832.01.NA.NA.NANA"
>>
>> I would have to reconvene with my instructor who wrote the original code
>> to determine what his desired output for the data would be, but from what I
>> can tell, this bit of coding is formatting the given dataset(s) that we are
>> working with, prepping them for what will be a Linear regression model of
>> the protein expression datatype contained with the larger dataset. Sorry, I
>> know that this explanation doesn't really narrow things down.
>>
>> For reference, here are the proceeding few lines of code following the
>> paste() function portion; specifically after the "})" ...
>>
>> exp = read.table(file =
>> "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/RNAseq/GBM.txt", sep = "\t",
>> header = T, row.names = 1)
>> exp = as.matrix(exp)
>> c = intersect(colnames(exp),colnames(meth))
>> exp = exp[,c]
>> meth = meth[,c]
>> m = apply(meth, 1, function(i){
>> log2(i/(1-i))
>> })
>>
>> Best,
>>
>> Spencer Brackett
>>
>> On Tue, Jun 25, 2019 at 4:54 PM Rui Barradas <ruipbarra...@sapo.pt>
>> wrote:
>>
>>> Hello,
>>>
>>> The following works.
>>> First, get the colnames you have posted in a format that R can process.
>>> in your code you would skip this.
>>>
>>> cnames <- scan(what = character(), text = '
>>> "sample.NA.NA.NANA"
>>> "TCGA.27.1832.01.NA.NA.NANA"
>>> "TCGA.27.1831.01.NA.NA.NANA"
>>> "TCGA.28.5216.01.NA.NA.NANA"
>>> "TCGA.16.0846.01.NA.NA.NANA"
>>> "TCGA.28.5218.01.NA.NA.NANA"
>>> "TCGA.06.0178.01.NA.NA.NANA"
>>> "TCGA.06.0238.01.NA.NA.NANA"
>>> "TCGA.06.0125.01.NA.NA.NANA"
>>> "TCGA.06.0219.01.NA.NA.NANA"
>>> ')
>>> cnames
>>>
>>>
>>> Now your code corrected. I do not understand the output you are
>>> expecting. Can you give an example of the expected output of, say, the
>>> first 2 or 3 strings?
>>>
>>> lapply(cnames, function(i){
>>> c1 <- strsplit(i, split = '\\.')[[1]]
>>> c1[4] <- paste(strsplit(c1[4], split = "",fixed = T)[[1]][1:2],
>>> collapse = "")
>>> paste(c1, collapse = ".")
>>> })
>>>
>>>
>>> Hope this helps,
>>>
>>> Rui Barradas
>>>
>>> Às 20:24 de 25/06/19, Spencer Brackett escreveu:
>>> > Mr. Barradas,
>>> >
>>> > Oh haha my mistake. The following is the output you requested....
>>> >
>>> > [1] "sample.NA.NA.NANA"
>>> > [2] "TCGA.27.1832.01.NA.NA.NANA"
>>> > [3] "TCGA.27.1831.01.NA.NA.NANA"
>>> > [4] "TCGA.28.5216.01.NA.NA.NANA"
>>> > [5] "TCGA.16.0846.01.NA.NA.NANA"
>>> > [6] "TCGA.28.5218.01.NA.NA.NANA"
>>> > [7] "TCGA.06.0178.01.NA.NA.NANA"
>>> > [8] "TCGA.06.0238.01.NA.NA.NANA"
>>> > [9] "TCGA.06.0125.01.NA.NA.NANA"
>>> > [10] "TCGA.06.0219.01.NA.NA.NANA"
>>> >
>>> > Best,
>>> >
>>> > Spencer
>>> >
>>> > On Tue, Jun 25, 2019 at 2:50 PM Rui Barradas <ruipbarra...@sapo.pt
>>> > <mailto:ruipbarra...@sapo.pt>> wrote:
>>> >
>>> > Hello,
>>> >
>>> > No, you have not understood, post the colnames, not the row.names.
>>> >
>>> > Run
>>> >
>>> > colnames(meth)[1:10]
>>> >
>>> > and post the output of that code line.
>>> >
>>> > Hope this helps,
>>> >
>>> > Rui Barradas
>>> >
>>> > Às 19:31 de 25/06/19, Spencer Brackett escreveu:
>>> > > The requested reprex....
>>> > >
>>> > > Rendering reprex...
>>> > > Error in parse(text = x, keep.source = TRUE) :
>>> > > <text>:26:2: unexpected ')'
>>> > > 25:
>>> > > 26: 2)
>>> > > ^
>>> > >
>>> > > And the subset of the data....
>>> > >
>>> > > row.names = c(NA, 6L), class = "data.frame")
>>> > >
>>> > > Best,
>>> > >
>>> > > Spencer
>>> > >
>>> > >
>>> > > On Tue, Jun 25, 2019 at 2:25 PM Rui Barradas
>>> > <ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
>>> > > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>>
>>> wrote:
>>> > >
>>> > > Hello,
>>> > >
>>> > > No I wasn't expecting a very large file.
>>> > > Try to make a reproducible example. If the problem seems to
>>> > be with the
>>> > > sapply/strsplit post a subset of the data like just some of
>>> the
>>> > > colnames:
>>> > >
>>> > > colnames(meth)[1:10]
>>> > >
>>> > >
>>> > > This would allow us to run the code you are having trouble
>>> with.
>>> > >
>>> > >
>>> > > Hope this helps,
>>> > >
>>> > > Rui Barradas
>>> > >
>>> > > Às 17:36 de 25/06/19, Spencer Brackett escreveu:
>>> > > > The result of dput(head(meth)) is a very large data
>>> > table/listing of
>>> > > > data by category of what I presume to be the data from
>>> the two
>>> > > TCGA .txt
>>> > > > files I referenced previously. Is this the output you
>>> were
>>> > expecting?
>>> > > >
>>> > > > On Tue, Jun 25, 2019 at 12:19 PM Rui Barradas
>>> > > <ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
>>> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>
>>> > > > <mailto:ruipbarra...@sapo.pt <mailto:
>>> ruipbarra...@sapo.pt>
>>> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>>>
>>> wrote:
>>> > > >
>>> > > > Hello,
>>> > > >
>>> > > > 1) That error comes from not closing }) after the
>>> paste()
>>> > > instruction.
>>> > > > The complete statement would be
>>> > > >
>>> > > >
>>> > > > colnames(meth) = sapply(colnames(meth), function(i){
>>> > > > c1 = strsplit(i, split ='\\', fixed = T)[[1]]
>>> > > > c1[4] = paste(strsplit(c1[4],split = "",fixed =
>>> > > > T)[[1]][1:2],collapse
>>> > > > = "")
>>> > > > paste(c1,collapse = ".")
>>> > > > })
>>> > > >
>>> > > >
>>> > > > 2) Can you post the output of the following?
>>> > > >
>>> > > > dput(head(meth))
>>> > > >
>>> > > >
>>> > > > Hope this helps,
>>> > > >
>>> > > > Rui Barradas
>>> > > >
>>> > > > Às 16:58 de 25/06/19, Spencer Brackett escreveu:
>>> > > > > The following is what I have implemented thus
>>> far...
>>> > > > >
>>> > > > > The file object for the two files listed in lines
>>> > 1-2 was
>>> > > set in my
>>> > > > > working directory, and are under the folder
>>> > "Vakul's GBM
>>> > > Code"...
>>> > > > hence
>>> > > > > the source of the odd 'prefix' for .txt files
>>> shown
>>> > > > >
>>> > > > > >library(data.table)>.anno =
>>> > as.data.frame(fread(file =
>>> > > > "~Vakul's GBM
>>> > > > > Code/mapper.txt", sep ="\t", header = T))
>>> > > > > >meth = read.table(file = "~Vakul's GBM
>>> Code/GBM.txt",
>>> > > sep ="\t",
>>> > > > > header = T, row.names = 1)
>>> > > > > >meth = as.matrix(meth)
>>> > > > >
>>> > > > > ## the loop just formats the methylation column
>>> > names to
>>> > > match
>>> > > > format ##
>>> > > > > colnames(meth) = sapply(colnames(meth),
>>> function(i){
>>> > > > > c1 = strsplit(i,split ='\\', fixed = T)[[1]]
>>> > > > > c1[4] = paste(strsplit(c1[4],split = "",fixed =
>>> > > > T)[[1]][1:2],collapse
>>> > > > > = "")
>>> > > > > paste(c1,collapse = ".")
>>> > > > >
>>> > > > > Rendering reprex...
>>> > > > > Error in parse(text = x, keep.source = TRUE) :
>>> > > > > <text>:28:0: unexpected end of input
>>> > > > >
>>> > > > > Best,
>>> > > > >
>>> > > > > Spencer
>>> > > > >
>>> > > > >
>>> > > > >
>>> > > > > On Tue, Jun 25, 2019 at 11:45 AM Spencer Brackett
>>> > > > > <spbracket...@saintjosephhs.com
>>> > <mailto:spbracket...@saintjosephhs.com>
>>> > > <mailto:spbracket...@saintjosephhs.com
>>> > <mailto:spbracket...@saintjosephhs.com>>
>>> > > > <mailto:spbracket...@saintjosephhs.com
>>> > <mailto:spbracket...@saintjosephhs.com>
>>> > > <mailto:spbracket...@saintjosephhs.com
>>> > <mailto:spbracket...@saintjosephhs.com>>>
>>> > > > <mailto:spbracket...@saintjosephhs.com
>>> > <mailto:spbracket...@saintjosephhs.com>
>>> > > <mailto:spbracket...@saintjosephhs.com
>>> > <mailto:spbracket...@saintjosephhs.com>>
>>> > > > <mailto:spbracket...@saintjosephhs.com
>>> > <mailto:spbracket...@saintjosephhs.com>
>>> > > <mailto:spbracket...@saintjosephhs.com
>>> > <mailto:spbracket...@saintjosephhs.com>>>>>
>>> > > > > wrote:
>>> > > > >
>>> > > > > Mr. Barradas,
>>> > > > >
>>> > > > > I got the same "output" as before, which is
>>> the +
>>> > > indicating that
>>> > > > > the expression is incomplete (according to
>>> some
>>> > R users
>>> > > > response in
>>> > > > > this chain).
>>> > > > >
>>> > > > > Should the argument perhaps be c1 =
>>> strsplit(i,
>>> > split
>>> > > = '\\',
>>> > > > fixed
>>> > > > > = T)[[1]] .... thereby eliminating the "." ?
>>> > > > > The reprex and error message as the result of
>>> > this is
>>> > > the same as
>>> > > > > the previous one I sent.
>>> > > > >
>>> > > > > I will send a more detailed description of
>>> what
>>> > code I
>>> > > have
>>> > > > done so
>>> > > > > far for context.
>>> > > > >
>>> > > > > Best,
>>> > > > >
>>> > > > > Spencer
>>> > > > >
>>> > > > > On Tue, Jun 25, 2019 at 11:30 AM Rui Barradas
>>> > > > <ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
>>> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>
>>> > > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
>>> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>>
>>> > > > > <mailto:ruipbarra...@sapo.pt
>>> > <mailto:ruipbarra...@sapo.pt>
>>> > > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>
>>> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
>>> > > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt
>>> >>>>>
>>> > > > wrote:
>>> > > > >
>>> > > > > Hello,
>>> > > > >
>>> > > > > Maybe with
>>> > > > >
>>> > > > > c1 = strsplit(i, split = '\\.', fixed =
>>> T)[[1]]
>>> > > > >
>>> > > > > instead of split = '.'
>>> > > > >
>>> > > > > The dot is a metacharacter that matches
>>> any
>>> > > character so
>>> > > > it has
>>> > > > > to be
>>> > > > > escaped.
>>> > > > >
>>> > > > > Hope this helps,
>>> > > > >
>>> > > > > Rui Barradas
>>> > > > >
>>> > > > > Às 16:11 de 25/06/19, Spencer Brackett
>>> > escreveu:
>>> > > > > > c1 = strsplit(i,split ='.', fixed =
>>> T)[[1]]
>>> > > > >
>>> > > >
>>> > >
>>> >
>>>
>>
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