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> 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>> 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>>>
> > > 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>>>
> > 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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