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